PMC20201220pmc.key5014086CC BYno2210.1016/j.str.2016.06.020501408627524201S0969-2126(16)30167-815999This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).1605surname:Zebisch;given-names:Matthiassurname:Jackson;given-names:Verity A.surname:Zhao;given-names:Yuguangsurname:Jones;given-names:E. YvonnePublished: August 11, 2016TITLEfront2420160Structure of the Dual-Mode Wnt Regulator Kremen1 and Insight into Ternary Complex Formation with LRP6 and Dickkopf0.99651647evidencecleaner02023-09-19T09:56:35ZDUMMY:Structureprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.998052proteincleaner02023-09-18T15:04:18ZPR:Kremen10.9978811proteincleaner02023-09-18T15:04:27ZPR:LRP60.99473995protein_typecleaner02023-09-18T15:10:24ZMESH:DickkopfABSTRACTabstract_title_1115SummaryABSTRACTabstract123Kremen 1 and 2 have been identified as co-receptors for Dickkopf (Dkk) proteins, hallmark secreted antagonists of canonical Wnt signaling. We present here three crystal structures of the ectodomain of human Kremen1 (KRM1ECD) at resolutions between 1.9 and 3.2 Å. KRM1ECD emerges as a rigid molecule with tight interactions stabilizing a triangular arrangement of its Kringle, WSC, and CUB structural domains. The structures reveal an unpredicted homology of the WSC domain to hepatocyte growth factor. We further report the general architecture of the ternary complex formed by the Wnt co-receptor Lrp5/6, Dkk, and Krm, determined from a low-resolution complex crystal structure between β-propeller/EGF repeats (PE) 3 and 4 of the Wnt co-receptor LRP6 (LRP6PE3PE4), the cysteine-rich domain 2 (CRD2) of DKK1, and KRM1ECD. DKK1CRD2 is sandwiched between LRP6PE3 and KRM1Kringle-WSC. Modeling studies supported by surface plasmon resonance suggest a direct interaction site between Krm1CUB and Lrp6PE2.0.99095875protein_typecleaner02023-09-18T15:12:16ZMESH:Kremen 1 and 20.92292756protein_typecleaner02023-09-18T15:04:40ZMESH:co-receptors0.9927476protein_typecleaner02023-09-18T15:10:24ZMESH:Dickkopf0.5698846protein_typecleaner02023-09-18T15:10:08ZMESH:Dkkprotein_typeMESH:cleaner02023-09-18T15:16:31ZWnt0.9986756evidencecleaner02023-09-18T15:08:21ZDUMMY:crystal structures0.9993445structure_elementcleaner02023-09-18T15:05:47ZSO:ectodomain0.99843925speciescleaner02023-09-18T15:05:25ZMESH:human0.9983398proteincleaner02023-09-18T15:04:18ZPR:Kremen1proteinPR:cleaner02023-09-18T15:06:10ZKRM1structure_elementSO:cleaner02023-09-18T15:06:25ZECDproteinPR:cleaner02023-09-18T15:06:40ZKRM1structure_elementSO:cleaner02023-09-18T15:06:49ZECD0.7506454protein_statecleaner02023-09-19T09:59:26ZDUMMY:triangular arrangement0.9995679structure_elementcleaner02023-09-18T15:07:03ZSO:Kringle0.9994825structure_elementcleaner02023-09-18T15:07:08ZSO:WSCstructure_elementSO:cleaner02023-09-18T15:07:23ZCUB0.99839205evidencecleaner02023-09-19T09:56:39ZDUMMY:structures0.9995127structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.84306806protein_typecleaner02023-09-19T09:54:50ZMESH:hepatocyte growth factorprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:17:09Zco-receptor0.9976937protein_typecleaner02023-09-19T08:37:55ZMESH:Lrp5/60.9320832protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.7082609protein_typecleaner02023-09-18T15:12:24ZMESH:Krm0.96125305evidencecleaner02023-09-18T15:08:17ZDUMMY:crystal structurestructure_elementSO:cleaner02023-09-18T15:11:48Zβ-propeller/EGF repeats (PE) 3 and 4protein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:17:09Zco-receptor0.99893945proteincleaner02023-09-18T15:04:28ZPR:LRP6proteinPR:cleaner02023-09-18T15:10:58ZLRP6structure_elementSO:cleaner02023-09-18T15:11:33ZPE3PE40.99921113structure_elementcleaner02023-09-18T15:05:11ZSO:cysteine-rich domain 20.99950767structure_elementcleaner02023-09-18T15:05:15ZSO:CRD20.9980861proteincleaner02023-09-19T08:56:11ZPR:DKK1proteinPR:cleaner02023-09-18T15:09:14ZKRM1structure_elementSO:cleaner02023-09-18T15:09:26ZECDproteinPR:cleaner02023-09-18T15:09:41ZDKK1structure_elementSO:cleaner02023-09-18T15:09:51ZCRD2proteinPR:cleaner02023-09-18T15:12:42ZLRP6structure_elementSO:cleaner02023-09-18T15:12:52ZPE3proteinPR:cleaner02023-09-19T10:02:17ZKRM1structure_elementSO:cleaner02023-09-19T10:02:42ZKringle-WSC0.5141169experimental_methodcleaner02023-09-19T10:03:07ZMESH:Modeling0.9983921experimental_methodcleaner02023-09-19T09:04:37ZMESH:surface plasmon resonance0.8810712sitecleaner02023-09-19T10:03:49ZSO:interaction siteproteinPR:cleaner02023-09-18T15:08:46ZKrm1structure_elementSO:cleaner02023-09-18T15:08:58ZCUBproteinPR:cleaner02023-09-18T15:13:25ZLrp6structure_elementSO:cleaner02023-09-18T15:13:34ZPE2ABSTRACTabstract_title_11127Graphical AbstractABSTRACTabstract_title_11146HighlightsABSTRACTabstract1157The structure of the KREMEN 1 ectodomain is solved from three crystal forms0.99753004evidencecleaner02023-09-18T15:13:54ZDUMMY:structure0.9986896proteincleaner02023-09-18T15:13:51ZPR:KREMEN 10.9994282structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.9849808experimental_methodcleaner02023-09-19T10:03:11ZMESH:solved0.99651587evidencecleaner02023-09-19T09:56:45ZDUMMY:crystal formsABSTRACTabstract1233Kringle, WSC, and CUB subdomains interact tightly to form a single structural unit0.99951434structure_elementcleaner02023-09-18T15:07:04ZSO:Kringle0.99952793structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.9995388structure_elementcleaner02023-09-18T15:18:34ZSO:CUBABSTRACTabstract1316The interface to DKKs is formed from the Kringle and WSC domains0.9988967sitecleaner02023-09-19T10:03:53ZSO:interface0.35081285protein_typecleaner02023-09-18T15:14:00ZMESH:DKKs0.9995615structure_elementcleaner02023-09-18T15:07:04ZSO:Kringle0.99953294structure_elementcleaner02023-09-18T15:07:09ZSO:WSCABSTRACTabstract1381The CUB domain is found to interact directly with LRP6PE1PE20.9994356structure_elementcleaner02023-09-18T15:18:34ZSO:CUBproteinPR:cleaner02023-09-18T15:14:18ZLRP6structure_elementSO:cleaner02023-09-18T15:14:27ZPE1PE2ABSTRACTabstract1442Zebisch et al. describe the ectodomain structure of KREMEN 1, a receptor for Wnt antagonists of the DKK family. Apo structures and a complex with functional fragments of DKK1 and LRP6 shed light on the function of this dual-mode regulator of Wnt signaling.0.99949515structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.9973246evidencecleaner02023-09-18T15:14:31ZDUMMY:structure0.9991677proteincleaner02023-09-18T15:14:34ZPR:KREMEN 10.6478protein_typecleaner02023-09-18T15:14:37ZMESH:receptorprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:15:03ZDKK0.99933225protein_statecleaner02023-09-18T15:15:08ZDUMMY:Apo0.9979297evidencecleaner02023-09-18T15:15:10ZDUMMY:structures0.98702407protein_statecleaner02023-09-18T15:15:14ZDUMMY:complex withprotein_stateDUMMY:cleaner02023-09-18T15:15:48Zfunctional fragments0.9988538proteincleaner02023-09-18T15:15:52ZPR:DKK10.9990638proteincleaner02023-09-18T15:04:28ZPR:LRP6protein_typeMESH:cleaner02023-09-18T15:16:32ZWntINTROtitle_11700IntroductionINTROparagraph1713Signaling by Wnt morphogens is renowned for its fundamental roles in embryonic development, tissue homeostasis, and stem cell maintenance. Due to these functions, generation, delivery, and interpretation of Wnt signals are all heavily regulated in the animal body. Vertebrate Dickkopf proteins (Dkk1, 2, and 4) are one of many secreted antagonists of Wnt and function by blocking access to the Wnt co-receptor LRP5/6. Kremen proteins (Krm1 and Krm2) have been identified as additional high-affinity transmembrane receptors for Dkk. Krm and Dkk synergize in Wnt inhibition during Xenopus embryogenesis to regulate anterior-posterior patterning. Mechanistically it is thought that, in the presence of Dkk, Krm forms a ternary complex with Lrp6, which is then rapidly endocytosed. This amplifies the intrinsic Wnt antagonistic activity of Dkk by efficiently depleting the cell surface of the Wnt co-receptor. In accordance with this, Krm1−/− and Krm2−/− double knockout mice show a high bone mass phenotype typical of increased Wnt signaling, as well as growth of ectopic forelimb digits. Growth of ectopic digits is further enhanced upon additional loss of dkk expression. The Wnt antagonistic activity of Krm1 is also linked to its importance for correct thymus epithelium formation in mice. The importance of intact KRM1 for normal human development and health is highlighted by the recent finding that a homozygous mutation in the ectodomain of KRM1 leads to severe ectodermal dysplasia including oligodontia. Interestingly, the Wnt antagonistic activity of Krm is context dependent, and Krm proteins are actually dual-mode Wnt regulators. In the absence of Dkk, Krm1 and 2 change their function from inhibition to enhancement of Lrp6-mediated signaling. By direct binding to Lrp6 via the ectodomains, Krm proteins promote Lrp6 cell-surface localization and hence increase receptor availability. Further increasing the complexity of Krm functionality, it was recently found that Krm1 (but not Krm2) can also act independently of LRP5/6 and Wnt as a dependence receptor, triggering apoptosis unless bound to Dkk.0.7128909protein_typecleaner02023-09-18T15:16:32ZMESH:Wnt0.44490612protein_typecleaner02023-09-18T15:16:32ZMESH:Wnt0.99849033taxonomy_domaincleaner02023-09-18T15:17:44ZDUMMY:Vertebrateprotein_typeMESH:cleaner02023-09-18T15:10:24ZDickkopf0.9958334protein_typecleaner02023-09-19T08:38:20ZMESH:Dkk10.8677284protein_typecleaner02023-09-19T08:38:27ZMESH:20.94611067protein_typecleaner02023-09-19T08:38:33ZMESH:40.87121487protein_typecleaner02023-09-18T15:16:32ZMESH:Wntprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:17:09Zco-receptor0.99744755proteincleaner02023-09-19T09:54:57ZPR:LRP5/6protein_typeMESH:cleaner02023-09-19T08:39:52ZKremen0.9968003protein_typecleaner02023-09-19T08:38:47ZMESH:Krm10.9968977protein_typecleaner02023-09-19T08:38:53ZMESH:Krm20.8356215protein_typecleaner02023-09-19T08:36:33ZMESH:transmembrane receptors0.9972887protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.99526924protein_typecleaner02023-09-19T09:53:34ZMESH:Krm0.9274017protein_typecleaner02023-09-18T15:10:08ZMESH:Dkkprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.9939586taxonomy_domaincleaner02023-09-18T15:17:49ZDUMMY:Xenopus0.9987738protein_statecleaner02023-09-19T08:34:48ZDUMMY:presence of0.9968412protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.71053296protein_typecleaner02023-09-19T09:53:37ZMESH:Krmprotein_stateDUMMY:cleaner02023-09-18T15:15:14Zcomplex with0.99414045protein_typecleaner02023-09-19T08:39:02ZMESH:Lrp6protein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.99530375protein_typecleaner02023-09-18T15:10:08ZMESH:Dkkprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:17:09Zco-receptorprotein_typeMESH:cleaner02023-09-19T08:39:11ZKrm1protein_typeMESH:cleaner02023-09-19T08:39:17ZKrm2experimental_methodMESH:cleaner02023-09-19T08:35:46Zdouble knockout0.9889488taxonomy_domaincleaner02023-09-19T08:36:13ZDUMMY:miceprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.97543895protein_typecleaner02023-09-19T08:39:26ZMESH:dkkprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.9871243protein_typecleaner02023-09-19T08:39:33ZMESH:Krm10.9975727taxonomy_domaincleaner02023-09-19T08:36:13ZDUMMY:mice0.9984781protein_statecleaner02023-09-19T09:59:31ZDUMMY:intact0.97736895proteincleaner02023-09-18T15:06:10ZPR:KRM10.9952508speciescleaner02023-09-18T15:05:25ZMESH:human0.9992774structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.9889864proteincleaner02023-09-18T15:06:10ZPR:KRM1protein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.99635315protein_typecleaner02023-09-19T09:53:41ZMESH:Krmprotein_typeMESH:cleaner02023-09-19T08:40:14ZKrm0.5892922protein_typecleaner02023-09-18T15:16:32ZMESH:Wnt0.9989779protein_statecleaner02023-09-19T09:24:47ZDUMMY:absence of0.9983632protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.9964774protein_typecleaner02023-09-19T08:40:38ZMESH:Krm10.95039356protein_typecleaner02023-09-19T08:40:46ZMESH:20.997929protein_typecleaner02023-09-19T08:41:23ZMESH:Lrp60.99880445protein_typecleaner02023-09-19T08:41:16ZMESH:Lrp60.99921465structure_elementcleaner02023-09-19T09:57:56ZSO:ectodomainsprotein_typeMESH:cleaner02023-09-19T08:40:29ZKrm0.9982597protein_typecleaner02023-09-19T08:40:56ZMESH:Lrp60.99672997protein_typecleaner02023-09-19T09:53:45ZMESH:Krm0.9892842protein_typecleaner02023-09-19T08:41:04ZMESH:Krm10.98860824protein_typecleaner02023-09-19T08:41:10ZMESH:Krm20.9977235proteincleaner02023-09-19T09:55:01ZPR:LRP5/60.5520213protein_typecleaner02023-09-18T15:16:32ZMESH:Wnt0.99863183protein_statecleaner02023-09-19T09:59:36ZDUMMY:bound to0.9985933protein_typecleaner02023-09-18T15:10:08ZMESH:DkkINTROparagraph3834Structurally, Krm1 and 2 are type I transmembrane proteins with a 40 kDa ectodomain and a flexible cytoplasmic tail consisting of 60–75 residues. The ectodomain consists of three similarly sized structural domains of around 10 kDa each: the N-terminal Kringle domain (KR) is followed by a WSC domain of unknown fold. The third structural domain is a CUB domain. An approximately 70-residue linker connects the CUB domain to the transmembrane span. An intact KR-WSC-CUB domain triplet and membrane attachment is required for Wnt antagonism. The transmembrane span and cytoplasmic tail can be replaced with a GPI linker without impact on Wnt antagonism.protein_typeMESH:cleaner02023-09-19T08:42:04ZKrm1protein_typeMESH:cleaner02023-09-19T08:42:15Z20.9981333protein_typecleaner02023-09-19T09:53:48ZMESH:type I transmembrane proteins0.99945766structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.9392079protein_statecleaner02023-09-19T09:59:42ZDUMMY:flexible0.9981252structure_elementcleaner02023-09-19T08:42:20ZSO:cytoplasmic tail0.8183996residue_rangecleaner02023-09-19T08:42:32ZDUMMY:600.6206278residue_rangecleaner02023-09-19T08:42:34ZDUMMY:750.99932384structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomainstructure_elementSO:cleaner02023-09-18T15:07:04ZKringle0.9994307structure_elementcleaner02023-09-18T15:18:39ZSO:KR0.9988023structure_elementcleaner02023-09-18T15:07:09ZSO:WSCstructure_elementSO:cleaner02023-09-18T15:18:34ZCUB0.6716569residue_rangecleaner02023-09-19T10:08:16ZDUMMY:approximately 70-residue0.98141634structure_elementcleaner02023-09-19T08:44:20ZSO:linker0.99934775structure_elementcleaner02023-09-18T15:18:33ZSO:CUB0.9992559structure_elementcleaner02023-09-19T08:44:30ZSO:transmembrane span0.9983392protein_statecleaner02023-09-19T09:59:46ZDUMMY:intactstructure_elementSO:cleaner02023-09-19T08:43:37ZKR-WSC-CUBprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.999244structure_elementcleaner02023-09-19T08:44:30ZSO:transmembrane span0.9991549structure_elementcleaner02023-09-19T08:43:12ZSO:cytoplasmic tailstructure_elementSO:cleaner02023-09-19T08:44:08ZGPIstructure_elementSO:cleaner02023-09-19T08:44:20Zlinkerprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntINTROparagraph4490We sought to provide structural insights into the multi-functionality of this cell-surface receptor. The structures presented here reveal the unknown fold of the WSC domain and the tight interactions of all three domains. We further succeeded in determination of a low-resolution LRP6PE3PE4-DKK1CRD2-KRM1ECD complex, defining the architecture of the Wnt inhibitory complex that leads to Lrp6 cell-surface depletion.0.9981673evidencecleaner02023-09-19T08:44:35ZDUMMY:structures0.9994917structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.99919complex_assemblycleaner02023-09-19T08:45:00ZGO:LRP6PE3PE4-DKK1CRD2-KRM1ECD0.5890333protein_typecleaner02023-09-18T15:16:32ZMESH:Wnt0.6935159complex_assemblycleaner02023-09-19T10:08:21ZGO:inhibitory complex0.99836403proteincleaner02023-09-18T15:04:28ZPR:Lrp6RESULTStitle_14907ResultsRESULTSparagraph4915The recombinant production of the extracellular domain of Krm for structural studies proved challenging (see Experimental Procedures). We succeeded in purifying KRM1ECD complexes with DKK1fl, DKK1Linker-CRD2, and DKK1CRD2 that were monodisperse and stable in gel filtration, hence indicating at least micromolar affinity (data not shown). Several crystal forms were obtained from these complexes, however, crystals always contained only KRM1 protein.0.99909973structure_elementcleaner02023-09-19T08:45:10ZSO:extracellular domain0.97918665protein_typecleaner02023-09-19T09:53:54ZMESH:Krmexperimental_methodMESH:cleaner02023-09-19T08:45:21Zstructural studiesproteinPR:cleaner02023-09-19T08:46:05ZKRM1structure_elementSO:cleaner02023-09-19T08:46:16ZECD0.72899675protein_statecleaner02023-09-19T08:45:34ZDUMMY:complexes with0.85313314proteincleaner02023-09-19T08:46:23ZPR:DKK1flproteinPR:cleaner02023-09-19T08:46:42ZDKK1structure_elementSO:cleaner02023-09-19T08:47:00ZLinker-CRD2proteinPR:cleaner02023-09-19T08:47:15ZDKK1structure_elementSO:cleaner02023-09-19T08:47:24ZCRD20.96971107experimental_methodcleaner02023-09-19T08:47:29ZMESH:gel filtration0.99780023evidencecleaner02023-09-19T08:47:34ZDUMMY:crystal forms0.9982065evidencecleaner02023-09-19T08:47:36ZDUMMY:crystals0.99675816proteincleaner02023-09-18T15:06:10ZPR:KRM1RESULTSparagraph5366We solved the structure of KRM1ECD in three crystal forms at 1.9, 2.8, and 3.2 Å resolution (Table 1). The high-resolution structure is a near full-length model (Figure 1). The small, flexible, and charged 98AEHED102 loop could only be modeled in a slightly lower resolution structure and in crystal form III. The KR, WSC, and CUB are arranged in a roughly triangular fashion with tight interactions between all three domains. The KR domain, which bears two of the four glycosylation sites, contains the canonical three disulfide bridges (C32-C114, C55-C95, C84-C109) and, like other Kringle domains, is low in secondary structure elements. The structurally most similar Kringle domain is that of human plasminogen (PDB: 1PKR) with an root-mean-square deviation (RMSD) of 1.7 Å for 73 aligned Cα (Figure 1B). The KRM1 structure reveals the fold of the WSC domain for the first time. The structure is best described as a sandwich of a β1-β5-β3-β4-β2 antiparallel β sheet and a single α helix. The structure is also rich in loops and is stabilized by four disulfide bridges (C122-C186, C147-C167, C151-C169, C190-C198). Using the PDBeFold server, we detected a surprising yet significant homology to PAN module domains. The closest structural relative is hepatocyte growth factor (HGF, PDB: 1GP9), which superposes with an RMSD of 2.3 Å for 58 aligned Cα (Figure 1B). The CUB domain bears two glycosylation sites. Although present, the quality of the electron density around N217 did not allow modeling of the sugar moiety. In crystal form I, a calcium ion is present at the canonical position coordinated by the carboxylates of D263, D266 (bidentate), and D306, as well as the carbonyl of N309 and a water molecule. The coordination sphere deviates significantly from perfectly octahedral (not shown). This might result in the site having a low affinity and may explain why calcium is not present in the two low-resolution crystal forms. Loss of calcium has led to loop rearrangements and partial disorder in these crystal forms. The closest structural relative is the CUB_C domain of Tsg-6 (PDB: 2WNO), which superposes with KRMCUB with an RMSD of 1.6 Å for 104 Cα (Figure 1B).0.99417144experimental_methodcleaner02023-09-19T08:47:44ZMESH:solved0.9750115evidencecleaner02023-09-19T08:47:47ZDUMMY:structureproteinPR:cleaner02023-09-19T08:48:04ZKRM1structure_elementSO:cleaner02023-09-19T08:48:15ZECD0.99771154evidencecleaner02023-09-19T08:48:23ZDUMMY:structure0.8854561protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.6456017protein_statecleaner02023-09-19T08:48:33ZDUMMY:small0.7668342protein_statecleaner02023-09-19T08:48:35ZDUMMY:flexibleprotein_stateDUMMY:cleaner02023-09-19T08:48:44Zcharged0.7967241structure_elementcleaner02023-09-19T08:48:47ZSO:98AEHED102 loop0.9976132evidencecleaner02023-09-19T08:48:50ZDUMMY:structure0.99952567structure_elementcleaner02023-09-18T15:18:39ZSO:KR0.9994319structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.99950206structure_elementcleaner02023-09-18T15:18:34ZSO:CUB0.99954283structure_elementcleaner02023-09-18T15:18:39ZSO:KR0.97424126sitecleaner02023-09-19T08:48:55ZSO:glycosylation sites0.9827687ptmcleaner02023-09-19T08:48:58ZMESH:disulfide bridges0.81650156residue_name_numbercleaner02023-09-19T10:13:48ZDUMMY:C320.90148216residue_name_numbercleaner02023-09-19T10:13:50ZDUMMY:C1140.6435744residue_name_numbercleaner02023-09-19T10:13:53ZDUMMY:C550.75450325residue_name_numbercleaner02023-09-19T10:13:55ZDUMMY:C950.6541933residue_name_numbercleaner02023-09-19T10:13:57ZDUMMY:C840.8610776residue_name_numbercleaner02023-09-19T10:14:00ZDUMMY:C109structure_elementSO:cleaner02023-09-18T15:07:04ZKringlestructure_elementSO:cleaner02023-09-18T15:07:04ZKringle0.99850476speciescleaner02023-09-18T15:05:25ZMESH:human0.9979559proteincleaner02023-09-19T09:56:05ZPR:plasminogen0.9984431evidencecleaner02023-09-19T08:51:04ZDUMMY:root-mean-square deviation0.9980584evidencecleaner02023-09-19T08:51:08ZDUMMY:RMSD0.8692057proteincleaner02023-09-18T15:06:10ZPR:KRM10.99708325evidencecleaner02023-09-19T08:51:18ZDUMMY:structure0.9993562structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.992714evidencecleaner02023-09-19T09:56:55ZDUMMY:structure0.73130274structure_elementcleaner02023-09-19T08:51:25ZSO:sandwich0.9923544structure_elementcleaner02023-09-19T08:51:22ZSO:β1-β5-β3-β4-β2 antiparallel β sheet0.9976212structure_elementcleaner02023-09-19T08:51:30ZSO:α helix0.9763921evidencecleaner02023-09-19T09:56:58ZDUMMY:structure0.9804582structure_elementcleaner02023-09-19T08:51:38ZSO:loops0.9856801ptmcleaner02023-09-19T10:08:32ZMESH:disulfide bridges0.72613335residue_name_numbercleaner02023-09-19T10:14:03ZDUMMY:C1220.94427705residue_name_numbercleaner02023-09-19T10:14:05ZDUMMY:C1860.5842389residue_name_numbercleaner02023-09-19T10:14:08ZDUMMY:C1470.8603606residue_name_numbercleaner02023-09-19T10:14:10ZDUMMY:C1670.67103654residue_name_numbercleaner02023-09-19T10:14:12ZDUMMY:C1510.9187694residue_name_numbercleaner02023-09-19T10:14:14ZDUMMY:C1690.93349916residue_name_numbercleaner02023-09-19T10:14:16ZDUMMY:C1900.9895691residue_name_numbercleaner02023-09-19T10:14:19ZDUMMY:C1980.9920827experimental_methodcleaner02023-09-19T08:51:47ZMESH:PDBeFold server0.9095351structure_elementcleaner02023-09-19T09:58:04ZSO:PAN module domains0.99497193protein_typecleaner02023-09-19T09:56:16ZMESH:hepatocyte growth factor0.9981103protein_typecleaner02023-09-19T09:56:24ZMESH:HGF0.9525247experimental_methodcleaner02023-09-19T10:03:16ZMESH:superposes0.9979018evidencecleaner02023-09-19T08:51:09ZDUMMY:RMSD0.99952483structure_elementcleaner02023-09-18T15:18:34ZSO:CUB0.99711406sitecleaner02023-09-19T08:51:54ZSO:glycosylation sites0.9984067evidencecleaner02023-09-19T08:52:12ZDUMMY:electron density0.99945residue_name_numbercleaner02023-09-19T08:52:20ZDUMMY:N217evidenceDUMMY:cleaner02023-09-19T10:05:00Zcrystal form I0.998784chemicalcleaner02023-09-19T08:52:01ZCHEBI:calciumbond_interactionMESH:cleaner02023-09-19T10:04:19Zcoordinated by0.9993892residue_name_numbercleaner02023-09-19T08:52:24ZDUMMY:D2630.99938715residue_name_numbercleaner02023-09-19T08:52:27ZDUMMY:D2660.99941325residue_name_numbercleaner02023-09-19T08:52:32ZDUMMY:D3060.9994622residue_name_numbercleaner02023-09-19T09:14:57ZDUMMY:N3090.9988845chemicalcleaner02023-09-19T08:52:06ZCHEBI:water0.9685152sitecleaner02023-09-19T10:04:02ZSO:coordination sphere0.9983772chemicalcleaner02023-09-19T08:52:02ZCHEBI:calciumevidenceDUMMY:cleaner02023-09-19T10:05:50Zcrystal formsprotein_stateDUMMY:cleaner02023-09-19T10:06:03ZLoss of0.99770206chemicalcleaner02023-09-19T08:52:02ZCHEBI:calcium0.98493505structure_elementcleaner02023-09-19T09:58:11ZSO:loopevidenceDUMMY:cleaner02023-09-19T10:05:38Zcrystal formsstructure_elementSO:cleaner02023-09-19T08:53:11ZCUB_C0.99908274proteincleaner02023-09-19T08:53:15ZPR:Tsg-60.9811162experimental_methodcleaner02023-09-19T10:03:19ZMESH:superposesproteinPR:cleaner02023-09-19T08:53:33ZKRMstructure_elementSO:cleaner02023-09-19T08:53:41ZCUB0.9975447evidencecleaner02023-09-19T08:51:09ZDUMMY:RMSDRESULTSparagraph7578A superposition of the three KRM1 structures reveals no major structural differences (Figure 1C) as anticipated from the plethora of interactions between the three domains. Minor differences are caused by the collapse of the Ca2+ binding site in crystal forms II and III and loop flexibility in the KR domain. The F207S mutation recently found to cause ectodermal dysplasia in Palestinian families maps to the hydrophobic core of the protein at the interface of the three subdomains (Figure 1A). Such a mutation is bound to severely destabilize the protein structure of KRM1, leading to disturbance of its Wnt antagonistic, Wnt stimulatory, and Wnt independent activity.0.9984787experimental_methodcleaner02023-09-19T08:53:58ZMESH:superposition0.9964317proteincleaner02023-09-18T15:06:10ZPR:KRM10.9969331evidencecleaner02023-09-19T09:57:03ZDUMMY:structures0.99897766sitecleaner02023-09-19T10:04:45ZSO:Ca2+ binding site0.98170817evidencecleaner02023-09-19T08:54:20ZDUMMY:crystal forms II and III0.9801446structure_elementcleaner02023-09-19T09:58:17ZSO:loop0.9993906structure_elementcleaner02023-09-18T15:18:39ZSO:KR0.9988738mutantcleaner02023-09-19T08:54:11ZMESH:F207S0.53296876sitecleaner02023-09-19T08:54:24ZSO:hydrophobic core0.998882sitecleaner02023-09-19T08:54:26ZSO:interfaceprotein_stateDUMMY:cleaner02023-09-19T09:59:37Zbound to0.9980704proteincleaner02023-09-18T15:06:10ZPR:KRM1protein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntRESULTStitle_28251Low-Resolution Insight into Ternary Complex FormationRESULTSparagraph8305Co-crystallization of LRP6PE3PE4 with DKK1CRD2, and LRP6PE1 with an N-terminal peptide of DKK1 has provided valuable structural insight into direct Wnt inhibition by Dkk ligands. One face of the rather flat DKK1CRD2 fragment binds to the third β propeller of LRP6. Mutational analyses further implied that the LRP6PE3-averted face of DKK1CRD2 bears the Krm binding site, hence suggesting how Dkk can recruit both receptors into a ternary complex.0.9989608experimental_methodcleaner02023-09-19T08:54:37ZMESH:Co-crystallizationproteinPR:cleaner02023-09-19T08:55:01ZLRP6structure_elementSO:cleaner02023-09-19T08:55:12ZPE3PE4proteinPR:cleaner02023-09-19T08:55:27ZDKK1structure_elementSO:cleaner02023-09-19T08:55:37ZCRD2proteinPR:cleaner02023-09-19T08:55:52ZLRP6structure_elementSO:cleaner02023-09-19T08:56:03ZPE10.9981754proteincleaner02023-09-19T08:56:11ZPR:DKK1protein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.5106511protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.9107751protein_statecleaner02023-09-19T09:59:50ZDUMMY:flatproteinPR:cleaner02023-09-19T08:56:40ZDKK1structure_elementSO:cleaner02023-09-19T08:56:50ZCRD2protein_stateDUMMY:cleaner02023-09-19T10:00:11Zbinds to0.99904746structure_elementcleaner02023-09-19T08:56:21ZSO:third β propeller0.99905545proteincleaner02023-09-18T15:04:28ZPR:LRP60.99858415experimental_methodcleaner02023-09-19T08:56:24ZMESH:Mutational analysesproteinPR:cleaner02023-09-19T08:57:26ZLRP6structure_elementSO:cleaner02023-09-19T08:57:36ZPE3proteinPR:cleaner02023-09-19T08:57:04ZDKK1structure_elementSO:cleaner02023-09-19T08:57:14ZCRD20.9990976sitecleaner02023-09-19T08:59:34ZSO:Krm binding site0.9959565protein_typecleaner02023-09-18T15:10:08ZMESH:Dkkprotein_typeMESH:cleaner02023-09-19T08:59:53ZreceptorsRESULTSparagraph8755To obtain direct insight into ternary complex formation by Lrp5/6, Dkk, and Krm, we subjected an LRP6PE3PE4-DKK1fl-KRM1ECD complex to crystallization trials. Diffraction data collected from the resulting crystals were highly anisotropic with diffraction extending in the best directions to 3.5 Å and 3.7 Å but only to 6.4 Å in the third direction. Despite the lack of high-resolution diffraction, the general architecture of the ternary complex is revealed (Figure 2A). DKK1CRD2 binds to the top face of the LRP6 PE3 β propeller as described earlier for the binary complex. KRM1ECD does indeed bind on the opposite side of DKK1CRD2 with only its KR and WSC domains engaged in binding (Figure 2A). Although present in the complex subjected to crystallization, we observe no density that could correspond to CRD1 or the domain linker (L). We confirm that the CRD2 of DKK1 is required and sufficient for binding to KRM1: In surface plasmon resonance (SPR), we measured low micromolar affinity between full-length DKK1 and immobilized KRM1ECD (Figure 2B). A SUMO fusion of DKK1L-CRD2 displayed a similar (slightly higher) affinity. In contrast, a SUMO fusion of DKK1CRD1-L did not display binding for concentrations tested up to 325 μM (Figure 2B).0.9977992protein_typecleaner02023-09-19T09:00:59ZMESH:Lrp5/60.9974843protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.99199754protein_typecleaner02023-09-19T09:01:06ZMESH:Krm0.99846774complex_assemblycleaner02023-09-19T09:00:46ZGO:LRP6PE3PE4-DKK1fl-KRM1ECD0.99831676experimental_methodcleaner02023-09-19T09:01:09ZMESH:crystallization trials0.9906544evidencecleaner02023-09-19T09:01:13ZDUMMY:Diffraction data0.9968412evidencecleaner02023-09-19T09:01:15ZDUMMY:crystals0.6915508evidencecleaner02023-09-19T09:01:19ZDUMMY:diffractionproteinPR:cleaner02023-09-19T09:01:39ZDKK1structure_elementSO:cleaner02023-09-19T09:01:49ZCRD2protein_stateDUMMY:cleaner02023-09-19T10:00:12Zbinds to0.9993006proteincleaner02023-09-18T15:04:28ZPR:LRP6structure_elementSO:cleaner02023-09-19T09:18:50ZPE3structure_elementSO:cleaner02023-09-19T09:57:24Zβ propellerproteinPR:cleaner02023-09-19T09:02:28ZKRM1structure_elementSO:cleaner02023-09-19T09:02:38ZECDprotein_stateDUMMY:cleaner02023-09-19T10:00:33Zbind onproteinPR:cleaner02023-09-19T09:02:01ZDKK1structure_elementSO:cleaner02023-09-19T09:02:13ZCRD20.9995098structure_elementcleaner02023-09-18T15:18:40ZSO:KR0.9993789structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.9972345experimental_methodcleaner02023-09-19T10:03:24ZMESH:crystallization0.9782202evidencecleaner02023-09-19T09:57:08ZDUMMY:density0.9987436structure_elementcleaner02023-09-19T09:58:29ZSO:CRD10.7814616structure_elementcleaner02023-09-19T09:03:02ZSO:domain linker0.9993906structure_elementcleaner02023-09-19T09:03:09ZSO:L0.99893695structure_elementcleaner02023-09-18T15:05:16ZSO:CRD20.9989029proteincleaner02023-09-19T08:56:12ZPR:DKK10.9977888proteincleaner02023-09-18T15:06:10ZPR:KRM10.9989211experimental_methodcleaner02023-09-19T09:04:37ZMESH:surface plasmon resonance0.9985241experimental_methodcleaner02023-09-19T09:04:40ZMESH:SPR0.9858543evidencecleaner02023-09-19T09:04:29ZDUMMY:affinity0.99905944protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.99898297proteincleaner02023-09-19T08:56:12ZPR:DKK1proteinPR:cleaner02023-09-19T09:03:59ZKRM1structure_elementSO:cleaner02023-09-19T09:04:09ZECD0.9979876experimental_methodcleaner02023-09-19T09:04:13ZMESH:SUMO fusionstructure_elementSO:cleaner02023-09-19T09:03:44ZDKK1L-CRD20.98279107evidencecleaner02023-09-19T09:04:31ZDUMMY:affinity0.9980215experimental_methodcleaner02023-09-19T09:04:13ZMESH:SUMO fusion0.9986412structure_elementcleaner02023-09-19T09:05:18ZSO:DKK1CRD1-LRESULTSparagraph10014Overall, the DKK1-KRM1 interface is characterized by a large number of polar interactions but only few hydrophobic contacts (Figure 2C). The crystal structure gives an explanation for DKK1 loss-of-binding mutations identified previously: R191 of DKK1 forms a double salt bridge to D125 and E162 of KRM1 (Figure 2C). A charge reversal as in the mouse Dkk1 (mDkk1) R197E variant would severely disrupt the binding. Similarly, the K226 side chain of DKK1, which points to a small hydrophobic pocket on the surface of KRM1 formed by Y108, W94, and W106, forms salt bridges with the side chains of KRM1 D88 and D90. Again, a charge reversal as shown before for mDkk1 K232E would be incompatible with binding. The side chain of DKK1 S192 was also predicted to be involved in Krm binding. Indeed, we found (Figure 2C) that the side chain of D201 of KRM1 forms two hydrogen bonds to the side-chain hydroxyl and the backbone amide of S192 (mouse, S198). Additional polar interactions are formed between the N140, S163, and Y165 side chains of KRM1 and DKK1 backbone carbonyls of W206, L190, and C189, respectively. The carbonyl of DKK1 R224 is hydrogen bonded to Y105 and W106 of KRM1. We suspect that the Dkk charge reversal mutations performed in the murine background and shown to diminish Krm binding K211E and R203E (mouse K217E and R209E) do so likely indirectly by disruption of the Dkk fold. We further validated the DKK1 binding site on KRM1 by introducing glycosylation sites at the KR (90DVS92→NVS) and WSC (189VCF191→NCS) domains pointing toward DKK (Figures 2A and 2D). Introduction of N-linked glycans in protein-protein-binding sites is an established way of disrupting protein-binding interfaces. Both ectodomain mutants were secreted comparably with the wild-type, indicating correct folding, but failed to achieve any detectable binding in SPR using full-length DKK1 as analyte. In contrast, a mutant carrying an additional N-glycan outside the interface at the CUB domain (309NQA311→NQS), was wild-type-like in DKK1 binding (Figure 2D).0.9988619sitecleaner02023-09-19T09:05:43ZSO:DKK1-KRM1 interface0.9965975bond_interactioncleaner02023-09-19T09:05:48ZMESH:polar interactions0.99685144bond_interactioncleaner02023-09-19T09:05:51ZMESH:hydrophobic contacts0.99868906evidencecleaner02023-09-18T15:08:17ZDUMMY:crystal structure0.9990559proteincleaner02023-09-19T08:56:12ZPR:DKK10.9994848residue_name_numbercleaner02023-09-19T09:08:19ZDUMMY:R1910.9990158proteincleaner02023-09-19T08:56:12ZPR:DKK10.99034667bond_interactioncleaner02023-09-19T09:05:55ZMESH:salt bridge0.9994804residue_name_numbercleaner02023-09-19T09:08:23ZDUMMY:D1250.9994967residue_name_numbercleaner02023-09-19T09:08:27ZDUMMY:E1620.5185777proteincleaner02023-09-18T15:06:10ZPR:KRM1experimental_methodMESH:cleaner02023-09-19T09:11:06Zcharge reversal0.9976808taxonomy_domaincleaner02023-09-19T09:08:08ZDUMMY:mouse0.9989874proteincleaner02023-09-19T09:56:31ZPR:Dkk10.9891629proteincleaner02023-09-19T09:07:14ZPR:mDkk10.99904364mutantcleaner02023-09-19T09:07:25ZMESH:R197E0.9994855residue_name_numbercleaner02023-09-19T09:08:32ZDUMMY:K2260.998976proteincleaner02023-09-19T08:56:12ZPR:DKK10.7484227sitecleaner02023-09-19T09:06:18ZSO:hydrophobic pocket0.88917637proteincleaner02023-09-18T15:06:10ZPR:KRM10.9995097residue_name_numbercleaner02023-09-19T09:08:37ZDUMMY:Y1080.99953055residue_name_numbercleaner02023-09-19T09:08:53ZDUMMY:W940.99950445residue_name_numbercleaner02023-09-19T09:08:57ZDUMMY:W1060.9966936bond_interactioncleaner02023-09-19T09:05:59ZMESH:salt bridges0.9668133proteincleaner02023-09-18T15:06:10ZPR:KRM10.9995011residue_name_numbercleaner02023-09-19T09:09:01ZDUMMY:D880.99948114residue_name_numbercleaner02023-09-19T09:09:05ZDUMMY:D90experimental_methodMESH:cleaner02023-09-19T09:11:12Zcharge reversal0.96642536proteincleaner02023-09-19T09:07:14ZPR:mDkk10.9990295mutantcleaner02023-09-19T09:07:29ZMESH:K232E0.9990246proteincleaner02023-09-19T08:56:12ZPR:DKK10.99949574residue_name_numbercleaner02023-09-19T09:09:11ZDUMMY:S1920.7990252protein_typecleaner02023-09-19T09:06:54ZMESH:Krm0.99949014residue_name_numbercleaner02023-09-19T09:09:16ZDUMMY:D2010.92195415proteincleaner02023-09-18T15:06:10ZPR:KRM10.9971021bond_interactioncleaner02023-09-19T09:06:03ZMESH:hydrogen bonds0.9994716residue_name_numbercleaner02023-09-19T09:09:11ZDUMMY:S1920.9979194taxonomy_domaincleaner02023-09-19T09:08:08ZDUMMY:mouse0.99947363residue_name_numbercleaner02023-09-19T09:09:28ZDUMMY:S1980.99713284bond_interactioncleaner02023-09-19T09:05:48ZMESH:polar interactions0.9994918residue_name_numbercleaner02023-09-19T09:09:33ZDUMMY:N1400.9995009residue_name_numbercleaner02023-09-19T09:09:38ZDUMMY:S1630.9995003residue_name_numbercleaner02023-09-19T09:09:43ZDUMMY:Y1650.9794397proteincleaner02023-09-18T15:06:10ZPR:KRM10.9987478proteincleaner02023-09-19T08:56:12ZPR:DKK10.9995042residue_name_numbercleaner02023-09-19T09:09:49ZDUMMY:W2060.99952114residue_name_numbercleaner02023-09-19T09:09:53ZDUMMY:L1900.99949884residue_name_numbercleaner02023-09-19T09:09:57ZDUMMY:C1890.9989812proteincleaner02023-09-19T08:56:12ZPR:DKK10.9995389residue_name_numbercleaner02023-09-19T09:10:02ZDUMMY:R2240.9967333bond_interactioncleaner02023-09-19T09:07:42ZMESH:hydrogen bonded0.9995384residue_name_numbercleaner02023-09-19T09:10:06ZDUMMY:Y1050.999521residue_name_numbercleaner02023-09-19T09:08:58ZDUMMY:W1060.99098295proteincleaner02023-09-18T15:06:10ZPR:KRM10.97223186protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.9541311experimental_methodcleaner02023-09-19T10:03:28ZMESH:charge reversal mutations0.9982382taxonomy_domaincleaner02023-09-19T09:08:14ZDUMMY:murineprotein_typeMESH:cleaner02023-09-19T09:10:24ZKrm0.9989784mutantcleaner02023-09-19T09:10:29ZMESH:K211E0.9990165mutantcleaner02023-09-19T09:10:33ZMESH:R203E0.9978951taxonomy_domaincleaner02023-09-19T09:08:08ZDUMMY:mouse0.99902844mutantcleaner02023-09-19T09:10:37ZMESH:K217E0.9990754mutantcleaner02023-09-19T09:10:41ZMESH:R209E0.99816555protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.99893934sitecleaner02023-09-19T09:06:29ZSO:DKK1 binding site0.9929836proteincleaner02023-09-18T15:06:10ZPR:KRM10.4963542experimental_methodcleaner02023-09-19T10:03:32ZMESH:introducing0.9917952sitecleaner02023-09-19T08:51:54ZSO:glycosylation sites0.9976114structure_elementcleaner02023-09-18T15:18:40ZSO:KR0.6751963mutantcleaner02023-09-19T09:07:36ZMESH:90DVS92→NVS0.9923799structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.36564493mutantcleaner02023-09-19T09:11:29ZMESH:189VCF191→NCS0.99895453proteincleaner02023-09-18T15:08:02ZPR:DKK0.67046195ptmcleaner02023-09-19T09:11:42ZMESH:N-linked glycans0.9990034sitecleaner02023-09-19T09:06:33ZSO:protein-protein-binding sites0.9990411sitecleaner02023-09-19T09:06:39ZSO:protein-binding interfaces0.88388306structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.80331635protein_statecleaner02023-09-19T10:00:57ZDUMMY:mutants0.99901456protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-type0.99868995experimental_methodcleaner02023-09-19T09:04:41ZMESH:SPR0.998916protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.9990551proteincleaner02023-09-19T08:56:12ZPR:DKK10.98682505protein_statecleaner02023-09-19T09:12:34ZDUMMY:mutantptmMESH:cleaner02023-09-19T09:12:08ZN-glycan0.9977586sitecleaner02023-09-19T09:06:42ZSO:interface0.9992186structure_elementcleaner02023-09-18T15:18:34ZSO:CUB0.99892753mutantcleaner02023-09-19T09:12:18ZMESH:309NQA311→NQS0.9991409protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-type0.9986671proteincleaner02023-09-19T08:56:12ZPR:DKK1RESULTStitle_212076Identification of a Direct LRP6-KRM1 Binding Site0.9978304sitecleaner02023-09-19T09:12:46ZSO:LRP6-KRM1 Binding SiteRESULTSparagraph12126The LRP6PE3PE4-DKK1CRD2-KRM1ECD complex structure reveals no direct interactions between KRM1 and LRP6. We constructed in silico a ternary complex with a close to full-length LRP6 ectodomain (PE1PE2PE3PE4 horse shoe) similar to but without refinement against electron microscopy (EM) or small-angle X-ray scattering data. An auxiliary PE3PE4 fragment was superimposed via PE4 onto PE3 of the crystal structure, and the LRP6PE1PE2 structure was superimposed via PE2 onto PE3 of this auxiliary fragment (Figure 3A).0.999238complex_assemblycleaner02023-09-19T08:45:01ZGO:LRP6PE3PE4-DKK1CRD2-KRM1ECD0.96343386evidencecleaner02023-09-19T09:57:31ZDUMMY:structure0.9925793proteincleaner02023-09-18T15:06:10ZPR:KRM10.99859744proteincleaner02023-09-18T15:04:28ZPR:LRP6protein_stateDUMMY:cleaner02023-09-18T15:15:14Zcomplex with0.9976246protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.999175proteincleaner02023-09-18T15:04:28ZPR:LRP60.99937844structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomainstructure_elementSO:cleaner02023-09-19T09:13:50ZPE1PE2PE3PE4structure_elementSO:cleaner02023-09-19T09:14:01Zhorse shoe0.99863327experimental_methodcleaner02023-09-19T09:13:15ZMESH:electron microscopy0.9984401experimental_methodcleaner02023-09-19T09:13:18ZMESH:EM0.99649286experimental_methodcleaner02023-09-19T09:13:23ZMESH:small-angle X-ray scattering0.4334478structure_elementcleaner02023-09-19T09:13:09ZSO:PE3PE40.99877995experimental_methodcleaner02023-09-19T09:13:28ZMESH:superimposed0.99630725structure_elementcleaner02023-09-19T09:18:45ZSO:PE40.99660873structure_elementcleaner02023-09-19T09:18:50ZSO:PE30.99758327evidencecleaner02023-09-18T15:08:17ZDUMMY:crystal structureproteinPR:cleaner02023-09-19T09:14:17ZLRP6structure_elementSO:cleaner02023-09-19T09:14:30ZPE1PE20.9973882evidencecleaner02023-09-19T09:13:34ZDUMMY:structure0.9988292experimental_methodcleaner02023-09-19T09:13:28ZMESH:superimposed0.99678135structure_elementcleaner02023-09-19T09:25:11ZSO:PE20.99711955structure_elementcleaner02023-09-19T09:18:50ZSO:PE3RESULTSparagraph12642For this crude approximation of a true ternary complex, we noted very close proximity between the Ca2+-binding region of KRM1 and the top face of the PE2 β propeller of LRP6. The solvent-exposed residues R307, I308, and N309 of the central Ca2+-binding β connection loop of KRM1 would be almost ideally positioned for binding to this face, which is commonly used as a binding site on β propellers. Peptides containing arginine/lysine, isoleucine, and asparagine (consensus sequence N-X-I-(G)-R/K) are also employed by DKK1 and SOST to bind to LRP6 (albeit to propeller 1; Figure 3B). To support the hypothesis that KRM1CUB binds to LRP6PE2, we used SPR and compared binding of the wild-type and the GlycoCUB mutant of KRM1ECD (bearing an N-glycosylation site at N309) with a purified LRP6PE1PE2 fragment. Indeed, we found that in the absence of Dkk, KRM1ECD bound with considerable affinity to LRP6PE1PE2 (Figure 3C). In contrast, no saturable binding was observed between KRM1 and LRP6PE3PE4. Introduction of an N-glycosylation site at N309 in KRM1ECD abolished LRP6PE1PE2 binding (Figure 3C), while binding to DKK1 was unaffected (Figure 2D). We conclude that the predicted binding site between KRM1CUB and LRP6PE2 is a strong candidate for mediating the direct Lrp6-Krm interaction, which is thought to increase Wnt responsiveness by stabilizing Lrp6 at the cell surface. Further experiments are required to pinpoint the exact binding site. Although LRP6PE1 appears somewhat out of reach in the modeled ternary complex, it cannot be excluded as the Krm binding site in the ternary complex and LRP6-Krm binary complex. The presence of DKK may govern which propeller (PE1 versus PE2) of LRP6 is available for Krm binding.0.99889165sitecleaner02023-09-19T09:14:38ZSO:Ca2+-binding region0.70204115proteincleaner02023-09-18T15:06:10ZPR:KRM1structure_elementSO:cleaner02023-09-19T09:25:10ZPE2structure_elementSO:cleaner02023-09-19T09:25:23Zβ propeller0.99911326proteincleaner02023-09-18T15:04:28ZPR:LRP6protein_stateDUMMY:cleaner02023-09-19T10:04:32Zsolvent-exposed0.9994591residue_name_numbercleaner02023-09-19T09:14:49ZDUMMY:R3070.99941707residue_name_numbercleaner02023-09-19T09:14:53ZDUMMY:I3080.99950254residue_name_numbercleaner02023-09-19T09:14:56ZDUMMY:N309structure_elementSO:cleaner02023-09-19T09:15:38ZCa2+-binding β connection loop0.8115768proteincleaner02023-09-18T15:06:10ZPR:KRM10.998543sitecleaner02023-09-19T09:15:48ZSO:binding site0.99863666structure_elementcleaner02023-09-19T09:15:45ZSO:β propellers0.99799347residue_namecleaner02023-09-19T09:15:50ZSO:arginine0.997482residue_namecleaner02023-09-19T09:15:52ZSO:lysine0.99793506residue_namecleaner02023-09-19T09:15:54ZSO:isoleucine0.99770665residue_namecleaner02023-09-19T09:15:56ZSO:asparagine0.9350921structure_elementcleaner02023-09-19T10:07:14ZSO:N-X-I-(G)-R/K0.99911493proteincleaner02023-09-19T08:56:12ZPR:DKK10.999201proteincleaner02023-09-19T09:16:15ZPR:SOST0.99911827proteincleaner02023-09-18T15:04:28ZPR:LRP60.9990943structure_elementcleaner02023-09-19T09:58:40ZSO:propeller 1proteinPR:cleaner02023-09-19T09:25:38ZKRM1structure_elementSO:cleaner02023-09-19T09:25:48ZCUBprotein_stateDUMMY:cleaner02023-09-19T10:00:12Zbinds toproteinPR:cleaner02023-09-19T09:26:02ZLRP6structure_elementSO:cleaner02023-09-19T09:26:14ZPE20.99864656experimental_methodcleaner02023-09-19T09:04:41ZMESH:SPR0.99910635protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-type0.9700352protein_statecleaner02023-09-19T09:27:01ZDUMMY:GlycoCUB mutantproteinPR:cleaner02023-09-19T09:26:33ZKRM1structure_elementSO:cleaner02023-09-19T09:26:50ZECD0.9965527sitecleaner02023-09-19T09:16:02ZSO:N-glycosylation site0.9995345residue_name_numbercleaner02023-09-19T09:14:57ZDUMMY:N309proteinPR:cleaner02023-09-19T09:27:18ZLRP6structure_elementSO:cleaner02023-09-19T09:27:28ZPE1PE20.9990541protein_statecleaner02023-09-19T09:24:46ZDUMMY:absence of0.9986665protein_typecleaner02023-09-18T15:10:08ZMESH:DkkproteinPR:cleaner02023-09-19T09:27:42ZKRM1structure_elementSO:cleaner02023-09-19T09:27:53ZECD0.9928445protein_statecleaner02023-09-19T10:01:29ZDUMMY:bound0.9828691protein_statecleaner02023-09-19T10:01:32ZDUMMY:toproteinPR:cleaner02023-09-19T09:28:11ZLRP6structure_elementSO:cleaner02023-09-19T09:28:21ZPE1PE20.9926576proteincleaner02023-09-18T15:06:10ZPR:KRM1proteinPR:cleaner02023-09-19T09:28:36ZLRP6structure_elementSO:cleaner02023-09-19T09:28:47ZPE3PE40.78763753experimental_methodcleaner02023-09-19T10:03:39ZMESH:Introduction of0.997533sitecleaner02023-09-19T09:24:25ZSO:N-glycosylation site0.99951124residue_name_numbercleaner02023-09-19T09:14:57ZDUMMY:N309proteinPR:cleaner02023-09-19T09:29:03ZKRM1structure_elementSO:cleaner02023-09-19T09:29:13ZECDproteinPR:cleaner02023-09-19T09:29:54ZLRP6structure_elementSO:cleaner02023-09-19T09:30:05ZPE1PE20.9990681proteincleaner02023-09-19T08:56:12ZPR:DKK10.99861795sitecleaner02023-09-19T10:06:41ZSO:binding siteproteinPR:cleaner02023-09-19T09:29:27ZKRM1structure_elementSO:cleaner02023-09-19T09:29:37ZCUBproteinPR:cleaner02023-09-19T09:30:19ZLRP6structure_elementSO:cleaner02023-09-19T09:30:28ZPE20.972133complex_assemblycleaner02023-09-19T09:23:58ZGO:Lrp6-Krmprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.9983664proteincleaner02023-09-18T15:04:28ZPR:Lrp6siteSO:cleaner02023-09-19T10:07:56Zbinding siteproteinPR:cleaner02023-09-19T09:30:44ZLRP6structure_elementSO:cleaner02023-09-19T09:30:55ZPE10.9989984sitecleaner02023-09-19T10:08:07ZSO:Krm binding site0.9991382complex_assemblycleaner02023-09-19T09:31:01ZGO:LRP6-Krm0.99640095protein_statecleaner02023-09-19T08:34:49ZDUMMY:presence of0.998844proteincleaner02023-09-18T15:08:02ZPR:DKK0.9993789structure_elementcleaner02023-09-19T09:58:43ZSO:propeller0.99949026structure_elementcleaner02023-09-19T09:31:09ZSO:PE10.99948514structure_elementcleaner02023-09-19T09:25:11ZSO:PE20.99907756proteincleaner02023-09-18T15:04:28ZPR:LRP60.66727495protein_typecleaner02023-09-19T09:58:53ZMESH:KrmRESULTSparagraph14374Apparent binding across the proposed KRM1CUB-LRP6PE2 interface is expected to be higher once Krm is also cross-linked to LRP6PE3 via DKK1CRD2 (Figure 3D). Low-resolution negative-stain EM and small-angle X-ray scattering studies of LRP6PE1PE2PE3PE4, in isolation and in complex with Dkk1, plus negative-stain EM of full-length LRP6 ectodomain, have indicated curved, platform-like conformations but also potential flexibility between PE2 and PE3. It is therefore possible that the interplay of Krm and Dkk binding can promote changes in LRP6 ectodomain conformation with functional consequences; however, such ideas await investigation.0.9990089sitecleaner02023-09-19T10:08:10ZSO:KRM1CUB-LRP6PE2 interface0.9994892protein_typecleaner02023-09-19T09:59:04ZMESH:KrmproteinPR:cleaner02023-09-19T09:32:33ZLRP6structure_elementSO:cleaner02023-09-19T09:32:43ZPE3proteinPR:cleaner02023-09-19T09:32:57ZDKK1structure_elementSO:cleaner02023-09-19T09:33:06ZCRD20.9989036experimental_methodcleaner02023-09-19T09:32:16ZMESH:negative-stain EM0.9989684experimental_methodcleaner02023-09-19T09:13:24ZMESH:small-angle X-ray scatteringproteinPR:cleaner02023-09-19T09:33:25ZLRP6structure_elementSO:cleaner02023-09-19T09:33:35ZPE1PE2PE3PE40.9033568protein_statecleaner02023-09-19T09:31:44ZDUMMY:in isolation0.99816304protein_statecleaner02023-09-19T09:31:38ZDUMMY:in complex with0.9985501protein_typecleaner02023-09-19T09:33:12ZMESH:Dkk10.99890447experimental_methodcleaner02023-09-19T09:32:16ZMESH:negative-stain EM0.9991421protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.999263proteincleaner02023-09-18T15:04:28ZPR:LRP60.99935347structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.99760216protein_statecleaner02023-09-19T10:01:44ZDUMMY:curved0.9706499protein_statecleaner02023-09-19T10:01:49ZDUMMY:platform-like0.99944097structure_elementcleaner02023-09-19T09:25:11ZSO:PE20.9994288structure_elementcleaner02023-09-19T09:18:50ZSO:PE30.9995103protein_typecleaner02023-09-19T09:31:59ZMESH:Krm0.5479226protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.9992786proteincleaner02023-09-18T15:04:28ZPR:LRP60.9993906structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomainRESULTSparagraph15012Taken together, the structural and biophysical studies we report here extend our mechanistic understanding of Wnt signal regulation. We describe the ectodomain structure of the dual Wnt regulator Krm1, providing an explanation for the detrimental effect on health and development of a homozygous KRM1 mutation. We also reveal the interaction mode of Krm-Dkk and the architecture of the ternary complex formed by Lrp5/6, Dkk, and Krm. Furthermore, the ternary crystal structure has guided in silico and biophysical analyses to suggest a direct LRP6-KRM1 interaction site. Our findings provide a solid foundation for additional studies to probe how ternary complex formation triggers internalization, whereas Krm binding in the absence of Dkk stabilizes the Wnt co-receptor at the cell surface.0.9987791experimental_methodcleaner02023-09-19T09:33:43ZMESH:structural and biophysical studiesprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.99944466structure_elementcleaner02023-09-18T15:05:48ZSO:ectodomain0.98785317evidencecleaner02023-09-19T09:57:37ZDUMMY:structureprotein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.99765694protein_typecleaner02023-09-19T09:33:57ZMESH:Krm10.9876721proteincleaner02023-09-18T15:06:10ZPR:KRM1complex_assemblyGO:cleaner02023-09-19T09:34:21ZKrm-Dkk0.9881404protein_typecleaner02023-09-19T09:34:07ZMESH:Lrp5/60.9984548protein_typecleaner02023-09-18T15:10:08ZMESH:Dkk0.9982216protein_typecleaner02023-09-19T09:34:29ZMESH:Krm0.9973328evidencecleaner02023-09-18T15:08:17ZDUMMY:crystal structure0.9021877experimental_methodcleaner02023-09-19T09:33:45ZMESH:in silico and biophysical analyses0.97991484sitecleaner02023-09-19T09:34:38ZSO:LRP6-KRM1 interaction site0.833017protein_typecleaner02023-09-19T09:34:54ZMESH:Krm0.9991188protein_statecleaner02023-09-19T09:24:47ZDUMMY:absence of0.9983999protein_typecleaner02023-09-18T15:10:08ZMESH:Dkkprotein_typeMESH:cleaner02023-09-18T15:16:32ZWntprotein_typeMESH:cleaner02023-09-18T15:17:09Zco-receptorMETHODStitle_115806Experimental ProceduresMETHODStitle_215830Large-Scale Mammalian Expression and Protein PurificationMETHODSparagraph15888KrmECD fragments were cloned into pHLsec or variants thereof. Full ectodomain variants (e.g., KRM1 isoform 3, P30-T377) were well secreted into the conditioned medium (CM) of HEK293T cells, but exhibited extensive O-glycosylation (as judged from smeary bands in western blot), which would be detrimental to crystallization. Fragments truncated to the KR-WSC-CUB core gave sharp bands but were barely secreted. We therefore engineered an A23-G373 (isoform 1 numbering used throughout the article) full ectodomain construct (KRM1ECD-TEV) with a C-terminal His10 tag that contained a TEV protease cleavage site after E324. The expected sequence of the secreted protein is ETG-23APSPGLGPGPE31 … 320AVKEE324-GSENLYFQGGS-325LPQ … VPG373-THHHHHHHHHH (the isoform-2-specific PG insertion and the TEV site are underlined). This construct was well secreted and could be processed using TEV protease. However, 80%–90% of the protein eluted as aggregates from a size-exclusion column even before TEV treatment. The same applied to analog constructs for Krm1 from zebrafish, frog, and mouse. No monomeric protein at all could be obtained for several Krm2 constructs from multiple species. A KRM1ECD-TEV expressing stable GntI-deficient HEK293S cell line was generated by excision of an EcoRI-XhoI fragment, sub-cloning into pNeo-Sec-1, and selection of neomycin-resistant cells. The stable cell line showed expression levels superior to transiently transfected cells (not shown).METHODSparagraph17365Human LRP6PE1PE2, LRP6PE3PE4, and full-length DKK1 were produced in a similar way as described. Shorter constructs of DKK1 lacking the N-terminal flexible region and CRD1 were not secreted from HEK cells. However, using the approach of an N-terminal fusion to a modified SUMO protein as described earlier, we succeeded in secretory expression of a SUMO-DKK1Linker-CRD2 construct encompassing residues S141-H266. A variant of this containing a TEV cleavage site just before T181, SUMO-DKK1Linker-TEV-CRD2, was also well expressed and allowed removal of the flexible linker region.METHODSparagraph17945To obtain complexes of KRM1ECD-TEV, we (co-)transfected the stable cell line with DKK and LRP6PE3PE4 constructs described earlier. Binary and ternary KRM1ECD-DKK1fl and KRM1ECD-DKK1fl-LRP6PE3PE4 complexes were stable in gel-filtration eluting as distinct monodisperse peaks.METHODStitle_218220Crystallization and Data CollectionMETHODSparagraph18256All samples subjected to crystallization were purified from CM by affinity and size-exclusion chromatography. After treatment with TEV protease and endoglycosidase F1 overnight using mass equivalents of 1%, samples were subjected to size-exclusion chromatography in 10 mM HEPES/NaOH (pH 7.5), 150 mM NaCl. The crystals giving rise to the 1.9 Å dataset for KRM1 in crystal form I were obtained from a KRM1ECD-DKK1Linker-CRD2 complex concentrated to 12 mg/mL. Out of this complex, KRM1ECD crystallized alone in 2.0 M ammonium sulfate, 5% (v/v) iso-propanol. For cryoprotection, crystals were transferred to mother liquor mixed 1:1 with 3.4 M sodium malonate (pH 7.0). The slightly less well-ordered crystal of crystal form I and crystals of form II were obtained from a KRM1ECD-DKK1CRD2 complex using the SUMO-DKK1Linker-TEV-CRD2 construct and releasing SUMO and the DKK linker region by TEV and 3C protease treatment. Crystals of form I (2.1 Å) appeared from protein at 12 mg/mL in 1.0 M (NH4)H2PO4, 0.100 M sodium citrate (pH 5.6) and were cryoprotected by transfer to 2.9 M sodium malonate (pH 5.0). Crystals of form II grew from protein concentrated to 17 mg/mL in 1.0 M MgSO4, 0.1 M trisodium citrate (final pH 5.6). For cryoprotection, crystals were transferred to mother liquor mixed 1:3 with 3.0 M ammonium sulfate, 18% glycerol. Crystal form III appeared after 11 months in a dried-out drop of condition H5 of the Morpheus screen. The protein concentration had been 9 mg/mL. For cryoprotection, fresh liquid from Morpheus/H5 was added. The ternary complex structure was obtained from an LRP6PE3PE4-DKK1fl-KRM1ECD complex at 9 mg/mL that grew in condition E10 of the PACTpremier screen (pH approximately 6.8) over the course of 2–11 months. For cryoprotection, 10% PEG200 was added. By mistake, the crystals were incubated for 1 hr with 1 mM platinum compound in this cryosolution before cryocooling.METHODStitle_220188Structure DeterminationMETHODSparagraph20212Diffraction data were collected at DIAMOND synchrotron light source at the beamlines detailed in Table 1. The structure was initially solved from crystal form III by molecular replacement (MR) with PHASER, placing models for the CUB domain (PDB: 2WNO, CUB_C domain of Tsg-6, 37% sequence identity), and the KR domain (PDB: 1PKR, Kringle 1 of plasminogen; 39% sequence identity). Traceable density for the WSC domain became immediately evident. The KRM1 structure was then built and refined by cycling between the various crystal forms.METHODSparagraph20748For the ternary complex, we obtained only a low-resolution, highly anisotropic dataset extending to Bragg spacings of 3.5 Å, 6.4 Å, and 3.7 Å along the three principle directions (<I/σI> = 2). All data to 3.5 Å were used during structure determination by MR. LRP6PE3PE4 (PDB: 4A0P) and KRM1ECD (both stripped of glycosylation sites) could be placed independently by PHASER, giving Z scores of >10 and log likelihood gains (LLG) of >200. The combined LLG was 673, increasing to 901 after rigid-body refinement. Strong electron density became apparent at glycosylation sites and close to methionines (see platinum soak above), further supporting the MR solution. Additional strong density was evident between LRP6 and KRM1, suggesting the presence of DKK1. A model of the DKK1CRD2 (PDB: 3S2K and 3S8V) could then be placed with PHASER by testing all rotation function peaks. This increased the LLG from 901 to 973 indicating a correct solution. The individually placed LRP6 and DKK models were then replaced with chains B and C from the LRP6-DKK complex in PDB: 3S2K. The structure was subjected to rigid-body refinement using single structural domains as individually positioned bodies.METHODSparagraph21945We then performed restrained refinement of the coordinates against the ellipsoidally truncated and anisotropically scaled diffraction data as obtained from the diffraction anisotropy server at UCLA. The resolution cutoffs were 3.5 Å, 6.4 Å, and 3.7 Å. Strong geometric restraints generated by PROSMART from the available high-resolution reference structures were used during refinement. No manual model building was attempted. Restrained refinement was followed by ten cycles of structure idealization. The final model had Rwork/Rfree errors of 32.5%/36.1% against the anisotropy-corrected data and 32.1%/35.5% against the unmodified but ellipsoidally truncated diffraction data.METHODStitle_222631Surface Plasmon ResonanceMETHODSparagraph22657Equilibrium experiments were performed as described before with the addition of 2 mM CaCl2 for experiments investigating the direct LRP6PE1PE2-KRM1ECD interaction.AUTH_CONTtitle_122822Author ContributionsAUTH_CONTparagraph22843M.Z. and V.A.J. performed experiments with support from Y.Z., who generated the stable cell line. M.Z. and E.Y.J. designed the research. M.Z. wrote the paper with input from all other authors.REFtitle23036References862873surname:Ahn;given-names:V.E.surname:Chu;given-names:M.L.surname:Choi;given-names:H.J.surname:Tran;given-names:D.surname:Abo;given-names:A.surname:Weis;given-names:W.I.22000856REFDev. 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Commun.ref4201326614Structural and molecular basis of ZNRF3/RNF43 transmembrane ubiquitin ligase inhibition by the Wnt agonist R-spondinKEYWORDtitle_126731Accession NumbersKEYWORDparagraph26749Coordinates and structure factors have been deposited in the PDB with succession numbers PDB: 5FWS, 5FWT, 5FWU, 5FWV, and 5FWW.SUPPLtitle_126877Supplemental InformationSUPPLfootnote26902Supplemental Information includes one figure and can be found with this article online at http://dx.doi.org/10.1016/j.str.2016.06.020.gr1.jpgfig1FIGfig_caption27037Structure of Unliganded KRM1ECD0.99732375evidencecleaner02023-09-19T09:57:41ZDUMMY:Structure0.9991748protein_statecleaner02023-09-19T09:42:59ZDUMMY:UnligandedproteinPR:cleaner02023-09-19T09:43:13ZKRM1structure_elementSO:cleaner02023-09-19T09:43:23ZECDgr1.jpgfig1FIGfig_caption27069(A) The KRM1ECD fold (crystal form I) colored blue to red from the N to C terminus. Cysteines as ball and sticks, glycosylation sites as sticks. The bound calcium is shown as a gray sphere. The site of the F207S mutation associated with ectodermal dysplasia in humans is shown as mesh.proteinPR:cleaner02023-09-19T09:43:40ZKRM1structure_elementSO:cleaner02023-09-19T09:43:49ZECDevidenceDUMMY:cleaner02023-09-19T09:43:59Zcrystal form I0.9921405residue_namecleaner02023-09-19T09:44:02ZSO:Cysteines0.9977498sitecleaner02023-09-19T08:51:54ZSO:glycosylation sites0.9988972chemicalcleaner02023-09-19T08:52:02ZCHEBI:calcium0.9986633mutantcleaner02023-09-19T08:54:12ZMESH:F207S0.99778545speciescleaner02023-09-19T09:44:11ZMESH:humansgr1.jpgfig1FIGfig_caption27356(B) Superposition of the three KRM1ECD subdomains (solid) with their next structurally characterized homologs (half transparent).0.99862194experimental_methodcleaner02023-09-19T08:53:58ZMESH:SuperpositionproteinPR:cleaner02023-09-19T09:44:31ZKRM1structure_elementSO:cleaner02023-09-19T09:44:47ZECDgr1.jpgfig1FIGfig_caption27486(C) Superposition of KRM1ECD from the three crystal forms. Alignment scores for each pairing are indicated on the dashed triangle.0.9977836experimental_methodcleaner02023-09-19T08:53:58ZMESH:SuperpositionproteinPR:cleaner02023-09-19T09:45:03ZKRM1structure_elementSO:cleaner02023-09-19T09:45:14ZECDevidenceDUMMY:cleaner02023-09-19T09:45:30Zcrystal forms0.9983538evidencecleaner02023-09-19T09:45:32ZDUMMY:Alignment scoresgr2.jpgfig2FIGfig_caption27617Insight into Ternary Complex Formationgr2.jpgfig2FIGfig_caption27656(A) The structure of the ternary LRP6PE3PE4-DKK1CRD2-KRM1ECD complex. DKK1 (orange) is sandwiched between the PE3 module of LRP6 (blue) and the KR-WSC domain pair of KRM1 (green). Colored symbols indicate introduced N-glycan attachment sites (see D).0.9669953evidencecleaner02023-09-19T09:45:40ZDUMMY:structure0.99905986complex_assemblycleaner02023-09-19T08:45:01ZGO:LRP6PE3PE4-DKK1CRD2-KRM1ECD0.99864715proteincleaner02023-09-19T08:56:12ZPR:DKK1structure_elementSO:cleaner02023-09-19T09:18:50ZPE30.9989537proteincleaner02023-09-18T15:04:28ZPR:LRP6structure_elementSO:cleaner02023-09-19T09:46:15ZKR-WSC0.8255878proteincleaner02023-09-18T15:06:11ZPR:KRM1siteSO:cleaner02023-09-19T09:46:51ZN-glycan attachment sitesgr2.jpgfig2FIGfig_caption27907(B) SPR data comparing binding of full-length DKK1 and SUMO fusions of DKK1 truncations for binding to immobilized wild-type KRM1ECD.0.99875593experimental_methodcleaner02023-09-19T09:04:41ZMESH:SPR0.999115protein_statecleaner02023-09-19T08:48:26ZDUMMY:full-length0.9985942proteincleaner02023-09-19T08:56:12ZPR:DKK10.9968902experimental_methodcleaner02023-09-19T10:03:44ZMESH:SUMO fusions0.9980323proteincleaner02023-09-19T08:56:12ZPR:DKK10.9991273protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-typeproteinPR:cleaner02023-09-19T09:47:07ZKRM1structure_elementSO:cleaner02023-09-19T09:47:17ZECDgr2.jpgfig2FIGfig_caption28041(C) Close-up view of the DKK1CRD2-KRM1ECD interface. Residues involved in interface formation are shown as sticks; those mentioned in the text are labeled. Salt bridges are in pink and hydrogen bonds in black. Model bias cannot be excluded as single atoms and bonds are not resolved at 6.4–3.5 Å. See also Figure S1.0.9989432sitecleaner02023-09-19T09:47:22ZSO:DKK1CRD2-KRM1ECD interface0.9983902sitecleaner02023-09-19T09:47:24ZSO:interface0.9784039bond_interactioncleaner02023-09-19T09:06:00ZMESH:Salt bridges0.9909836bond_interactioncleaner02023-09-19T09:06:04ZMESH:hydrogen bondsgr2.jpgfig2FIGfig_caption28364(D) SPR binding data comparing DKK1 analyte binding with wild-type KRM1ECD and three variants bearing engineered glycosylation sites on the KR and WSC domains (green and blue pointing to DKK1) and on the CUB domain (orange). See also symbols in (A).0.9901149experimental_methodcleaner02023-09-19T09:04:41ZMESH:SPR0.97566277evidencecleaner02023-09-19T09:47:35ZDUMMY:binding data0.99840933proteincleaner02023-09-19T08:56:12ZPR:DKK10.9990173protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-typeproteinPR:cleaner02023-09-19T09:47:52ZKRM1structure_elementSO:cleaner02023-09-19T09:48:05ZECD0.5362611protein_statecleaner02023-09-19T09:48:16ZDUMMY:engineered0.96274155sitecleaner02023-09-19T08:51:54ZSO:glycosylation sites0.9995296structure_elementcleaner02023-09-18T15:18:40ZSO:KR0.9994419structure_elementcleaner02023-09-18T15:07:09ZSO:WSC0.9988524proteincleaner02023-09-19T08:56:12ZPR:DKK10.9995295structure_elementcleaner02023-09-18T15:18:34ZSO:CUBgr3.jpgfig3FIGfig_caption28614LRP6-KRM1 Direct Interaction and Summarycomplex_assemblyGO:cleaner02023-09-19T09:48:37ZLRP6-KRM1gr3.jpgfig3FIGfig_caption28655(A) In a construction of a ternary complex with all four β propellers of LRP6 intact, the CUB domain points via its Ca2+-binding region toward the top face of the second β propeller.protein_stateDUMMY:cleaner02023-09-18T15:15:14Zcomplex with0.9945204structure_elementcleaner02023-09-19T09:59:08ZSO:β propellers0.9993331proteincleaner02023-09-18T15:04:28ZPR:LRP60.99916625protein_statecleaner02023-09-19T10:01:54ZDUMMY:intactstructure_elementSO:cleaner02023-09-18T15:18:34ZCUB0.9988576sitecleaner02023-09-19T09:48:54ZSO:Ca2+-binding region0.7878209structure_elementcleaner02023-09-19T09:59:12ZSO:second β propellergr3.jpgfig3FIGfig_caption28844(B) Close-up view of the potential interaction site. In addition, LRP6PE2 has been superimposed with DKK1 (yellow) and SOST (pink) peptide complexes of LRP6PE1.0.9988657sitecleaner02023-09-19T09:48:59ZSO:interaction siteproteinPR:cleaner02023-09-19T09:49:12ZLRP6structure_elementSO:cleaner02023-09-19T09:49:23ZPE20.9987097experimental_methodcleaner02023-09-19T09:13:28ZMESH:superimposed0.9986634proteincleaner02023-09-19T08:56:12ZPR:DKK10.9988487proteincleaner02023-09-19T09:16:16ZPR:SOSTproteinPR:cleaner02023-09-19T09:49:36ZLRP6structure_elementSO:cleaner02023-09-19T09:49:45ZPE1gr3.jpgfig3FIGfig_caption29005(C) SPR measurements comparing LRP6PE1PE2 binding with wild-type KRM1ECD and the GlycoCUB mutant bearing an N-glycan at N309.0.7926361experimental_methodcleaner02023-09-19T09:49:59ZMESH:SPR measurementsproteinPR:cleaner02023-09-19T09:50:12ZLRP6structure_elementSO:cleaner02023-09-19T09:50:22ZPE1PE20.9989366protein_statecleaner02023-09-19T09:12:22ZDUMMY:wild-typeproteinPR:cleaner02023-09-19T09:50:35ZKRM1structure_elementSO:cleaner02023-09-19T09:50:45ZECDprotein_stateDUMMY:cleaner02023-09-19T10:06:53ZGlycoCUB mutantptmMESH:cleaner02023-09-19T09:51:21ZN-glycan0.99950445residue_name_numbercleaner02023-09-19T09:14:57ZDUMMY:N309gr3.jpgfig3FIGfig_caption29131(D) Schematic representation of structural and biophysical findings and their implications for Wnt-dependent (left, middle) and independent (right) signaling. Conformational differences in the depictions of LRP6 are included purely for ease of representation.protein_typeMESH:cleaner02023-09-18T15:16:32ZWnt0.9989386proteincleaner02023-09-18T15:04:28ZPR:LRP6tbl1.xmltbl1TABLEtable_caption29391Diffraction and Refinement Statistics0.9977757evidencecleaner02023-09-19T09:57:47ZDUMMY:Diffraction and Refinement Statisticstbl1.xmltbl1TABLEtable<?xml version="1.0" encoding="UTF-8"?>
<table xmlns:xlink="http://www.w3.org/1999/xlink" frame="hsides" rules="groups"><thead><tr><th/><th>KRM1<sub>ECD</sub></th><th>KRM1<sub>ECD</sub></th><th>KRM1<sub>ECD</sub></th><th>KRM1<sub>ECD</sub></th><th>LRP6<sub>PE3PE4</sub>-DKK<sub>CRD2</sub>-KRM1<sub>ECD</sub></th></tr></thead><tbody><tr><td>Crystal form</td><td>I</td><td>I</td><td>II</td><td>III</td><td>I</td></tr><tr><td>X-ray source</td><td>Diamond i04</td><td>Diamond i03</td><td>Diamond i03</td><td>Diamond i04</td><td>Diamond i04</td></tr><tr><td>Wavelength (Å)</td><td>0.9793</td><td>0.9700</td><td>0.9700</td><td>0.9795</td><td>0.9795</td></tr><tr><td>Space group</td><td><italic>P</italic>3<sub>1</sub>21</td><td><italic>P</italic>3<sub>1</sub>21</td><td><italic>P</italic>4<sub>3</sub></td><td><italic>P</italic>4<sub>1</sub>2<sub>1</sub>2</td><td><italic>C</italic>222<sub>1</sub></td></tr><tr><td>Unit cell a/α (Å/°)</td><td>50.9/90</td><td>50.5/90</td><td>65.8/90</td><td>67.8/90</td><td>86.9/90</td></tr><tr><td>b/β (Å/°)</td><td>50.9/90</td><td>50.5/90</td><td>65.8/90</td><td>67.8/90</td><td>100.1/90</td></tr><tr><td>c/γ (Å/°)</td><td>188.4/120</td><td>187.4/120</td><td>75.0/90</td><td>198.2/90</td><td>270.7/90</td></tr><tr><td>Wilson B factor (Å<sup>2</sup>)</td><td>31</td><td>41</td><td>76</td><td>77</td><td>NA</td></tr><tr><td>Resolution range (Å)</td><td>47.10–1.90 (1.95–1.90)</td><td>62.47–2.10 (2.16–2.10)</td><td>75.00–2.80 (2.99–2.80)</td><td>67.80–3.20 (3.42–3.20)</td><td>67.68–3.50 (7.16–6.40, 3.92–3.50)</td></tr><tr><td>Unique reflections</td><td>23,300 (1,524)</td><td>17,089 (1,428)</td><td>7,964 (1,448)</td><td>8,171 (1,343)</td><td>8,070 (723, 645)</td></tr><tr><td>Average multiplicity</td><td>9.1 (9.2)</td><td>5.2 (5.3)</td><td>3.7 (3.7)</td><td>22.7 (12.6)</td><td>3.8 (3.5, 4.4)</td></tr><tr><td>Completeness (%)</td><td>99.8 (98.5)</td><td>100 (100)</td><td>99.8 (100)</td><td>98.8 (93.4)</td><td>51.6 (98.5, 14.1)</td></tr><tr><td><<italic>I</italic>/<italic>σI</italic>></td><td>11.4 (1.7)</td><td>12.0 (1.7)</td><td>14.9 (1.5)</td><td>13.1 (1.9)</td><td>4.6 (4.1, 2.2)</td></tr><tr><td><italic>R</italic><sub>merge</sub> (%)</td><td>14.8 (158.3)</td><td>9.3 (98.0)</td><td>6.2 (98.9)</td><td>29.8 (142.2)</td><td>44.9 (40.5, 114.2)</td></tr><tr><td><italic>R</italic><sub>pim</sub> (%)</td><td>15.7 (55.3)</td><td>10.3 (109.0)</td><td>3.7 (53.8)</td><td>6.3 (40.0)</td><td>24.7 (23.9, 59.9)</td></tr><tr><td colspan="6"><hr/></td></tr><tr><td colspan="6"><bold>Refinement</bold></td></tr><tr><td colspan="6"><hr/></td></tr><tr><td><italic>R</italic><sub>work</sub> (%)</td><td>17.9</td><td>18.4</td><td>21.6</td><td>20.2</td><td>32.1</td></tr><tr><td><italic>R</italic><sub>free</sub> (%)</td><td>22.7</td><td>23.2</td><td>30.7</td><td>27.1</td><td>35.5</td></tr><tr><td colspan="6"><hr/></td></tr><tr><td colspan="6"><bold>No. of Non-Hydrogen Atoms</bold></td></tr><tr><td colspan="6"><hr/></td></tr><tr><td>Protein</td><td>2,260</td><td>2,301</td><td>2,102</td><td>2,305</td><td>7,730</td></tr><tr><td>N-glycans</td><td>42</td><td>42</td><td>28</td><td>28</td><td>0</td></tr><tr><td>Water</td><td>79</td><td>54</td><td>0</td><td>2</td><td>0</td></tr><tr><td>Ligands</td><td>6</td><td>6</td><td>2</td><td>5</td><td>0</td></tr><tr><td colspan="6"><hr/></td></tr><tr><td colspan="6"><bold>Average B factor (Å<sup>2</sup>)</bold></td></tr><tr><td colspan="6"><hr/></td></tr><tr><td>Protein</td><td>63</td><td>65</td><td>108</td><td>84</td><td>–</td></tr><tr><td>N-glycans</td><td>35</td><td>46</td><td>102</td><td>18</td><td>–</td></tr><tr><td>Water</td><td>68</td><td>85</td><td>–</td><td>75</td><td>–</td></tr><tr><td>Ligands</td><td>36</td><td>47</td><td>91</td><td>75</td><td>66</td></tr><tr><td colspan="6"><hr/></td></tr><tr><td colspan="6"><bold>RMSD from Ideality</bold></td></tr><tr><td colspan="6"><hr/></td></tr><tr><td>Bond lengths (Å)</td><td>0.020</td><td>0.016</td><td>0.019</td><td>0.016</td><td>0.004</td></tr><tr><td>Bond angles (°)</td><td>2.050</td><td>1.748</td><td>1.952</td><td>1.796</td><td>0.770</td></tr><tr><td colspan="6"><hr/></td></tr><tr><td colspan="6"><bold>Ramachandran Plot</bold></td></tr><tr><td colspan="6"><hr/></td></tr><tr><td>Favored (%)</td><td>96.8</td><td>95.5</td><td>96.9</td><td>94.9</td><td>92.3</td></tr><tr><td>Allowed (%)</td><td>99.7</td><td>100.0</td><td>100.0</td><td>99.7</td><td>99.8</td></tr><tr><td>Number of outliers</td><td>1</td><td>0</td><td>0</td><td>1</td><td>2</td></tr><tr><td>PDB code</td><td><ext-link ext-link-type="uri" xlink:href="pdb:5FWS" id="intref0085">5FWS</ext-link></td><td><ext-link ext-link-type="uri" xlink:href="pdb:5FWT" id="intref0090">5FWT</ext-link></td><td><ext-link ext-link-type="uri" xlink:href="pdb:5FWU" id="intref0095">5FWU</ext-link></td><td><ext-link ext-link-type="uri" xlink:href="pdb:5FWV" id="intref0100">5FWV</ext-link></td><td><ext-link ext-link-type="uri" xlink:href="pdb:5FWW" id="intref0105">5FWW</ext-link></td></tr></tbody></table>
29429 KRM1ECD KRM1ECD KRM1ECD KRM1ECD LRP6PE3PE4-DKKCRD2-KRM1ECD Crystal form I I II III I X-ray source Diamond i04 Diamond i03 Diamond i03 Diamond i04 Diamond i04 Wavelength (Å) 0.9793 0.9700 0.9700 0.9795 0.9795 Space group P3121 P3121 P43 P41212 C2221 Unit cell a/α (Å/°) 50.9/90 50.5/90 65.8/90 67.8/90 86.9/90 b/β (Å/°) 50.9/90 50.5/90 65.8/90 67.8/90 100.1/90 c/γ (Å/°) 188.4/120 187.4/120 75.0/90 198.2/90 270.7/90 Wilson B factor (Å2) 31 41 76 77 NA Resolution range (Å) 47.10–1.90 (1.95–1.90) 62.47–2.10 (2.16–2.10) 75.00–2.80 (2.99–2.80) 67.80–3.20 (3.42–3.20) 67.68–3.50 (7.16–6.40, 3.92–3.50) Unique reflections 23,300 (1,524) 17,089 (1,428) 7,964 (1,448) 8,171 (1,343) 8,070 (723, 645) Average multiplicity 9.1 (9.2) 5.2 (5.3) 3.7 (3.7) 22.7 (12.6) 3.8 (3.5, 4.4) Completeness (%) 99.8 (98.5) 100 (100) 99.8 (100) 98.8 (93.4) 51.6 (98.5, 14.1) <I/σI> 11.4 (1.7) 12.0 (1.7) 14.9 (1.5) 13.1 (1.9) 4.6 (4.1, 2.2) Rmerge (%) 14.8 (158.3) 9.3 (98.0) 6.2 (98.9) 29.8 (142.2) 44.9 (40.5, 114.2) Rpim (%) 15.7 (55.3) 10.3 (109.0) 3.7 (53.8) 6.3 (40.0) 24.7 (23.9, 59.9) Refinement Rwork (%) 17.9 18.4 21.6 20.2 32.1 Rfree (%) 22.7 23.2 30.7 27.1 35.5 No. of Non-Hydrogen Atoms Protein 2,260 2,301 2,102 2,305 7,730 N-glycans 42 42 28 28 0 Water 79 54 0 2 0 Ligands 6 6 2 5 0 Average B factor (Å2) Protein 63 65 108 84 – N-glycans 35 46 102 18 – Water 68 85 – 75 – Ligands 36 47 91 75 66 RMSD from Ideality Bond lengths (Å) 0.020 0.016 0.019 0.016 0.004 Bond angles (°) 2.050 1.748 1.952 1.796 0.770 Ramachandran Plot Favored (%) 96.8 95.5 96.9 94.9 92.3 Allowed (%) 99.7 100.0 100.0 99.7 99.8 Number of outliers 1 0 0 1 2 PDB code 5FWS 5FWT 5FWU 5FWV 5FWW proteinPR:cleaner02023-09-19T09:51:42ZKRM1structure_elementSO:cleaner02023-09-19T09:51:53ZECDproteinPR:cleaner02023-09-19T09:52:10ZKRM1structure_elementSO:cleaner02023-09-19T09:52:20ZECDproteinPR:cleaner02023-09-19T09:52:35ZKRM1structure_elementSO:cleaner02023-09-19T09:52:45ZECDproteinPR:cleaner02023-09-19T09:52:57ZKRM1structure_elementSO:cleaner02023-09-19T09:53:06ZECD0.98330337complex_assemblycleaner02023-09-19T10:08:25ZGO:LRP6PE3PE4-DKKCRD2-KRM1ECDchemicalCHEBI:cleaner02023-09-19T08:52:06ZWaterchemicalCHEBI:cleaner02023-09-19T08:52:06ZWaterevidenceDUMMY:cleaner02023-09-19T08:51:09ZRMSDtbl1.xmltbl1TABLEtable_footnote31236Values in parentheses refer to the highest-resolution shell. An additional shell given for the ternary complex corresponds to the last shell with near-complete diffraction data. NA, not announced.0.7761474evidencecleaner02023-09-19T09:57:51ZDUMMY:diffraction data