PMC20201222pmc.key4781976CC BYno0010.1016/j.dib.2016.02.042478197626977434S2352-3409(16)30064-6344Tom1, GAT domain, Tollip, Ubiquitin, nuclear magnetic resonanceThis is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).348surname:Xiao;given-names:Shuyansurname:Ellena;given-names:Jeffrey F.surname:Armstrong;given-names:Geoffrey S.surname:Capelluto;given-names:Daniel G.S.TITLEKeywordsfront720160Structure of the GAT domain of the endosomal adapter protein Tom10.9991358evidencecleaner02023-07-20T14:57:22ZDUMMY:Structurestructure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.9416477protein_typecleaner02023-07-20T14:56:57ZMESH:adapter protein0.9997857proteincleaner02023-07-20T14:57:11ZPR:Tom1ABSTRACTabstract66Cellular homeostasis requires correct delivery of cell-surface receptor proteins (cargo) to their target subcellular compartments. The adapter proteins Tom1 and Tollip are involved in sorting of ubiquitinated cargo in endosomal compartments. Recruitment of Tom1 to the endosomal compartments is mediated by its GAT domain’s association to Tollip’s Tom1-binding domain (TBD). In this data article, we report the solution NMR-derived structure of the Tom1 GAT domain. The estimated protein structure exhibits a bundle of three helical elements. We compare the Tom1 GAT structure with those structures corresponding to the Tollip TBD- and ubiquitin-bound states.0.8085951protein_typecleaner02023-07-20T14:56:52ZMESH:cell-surface receptor0.99906075protein_typecleaner02023-07-20T14:57:01ZMESH:adapter proteins0.99983084proteincleaner02023-07-20T14:57:11ZPR:Tom10.99978274proteincleaner02023-07-20T14:57:16ZPR:Tollip0.96031576ptmcleaner02023-07-20T14:59:03ZMESH:ubiquitinated0.9998591proteincleaner02023-07-20T14:57:11ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.99981624proteincleaner02023-07-20T14:57:16ZPR:Tollip0.999658structure_elementcleaner02023-07-20T14:57:32ZSO:Tom1-binding domain0.9997849structure_elementcleaner02023-07-20T14:57:36ZSO:TBD0.9995477experimental_methodcleaner02023-07-20T15:00:01ZMESH:solution NMR0.9994789evidencecleaner02023-07-20T14:57:22ZDUMMY:structure0.9998665proteincleaner02023-07-20T14:57:11ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.999076evidencecleaner02023-07-20T14:57:22ZDUMMY:structure0.917164experimental_methodcleaner02023-07-20T15:06:26ZMESH:compare0.9998603proteincleaner02023-07-20T14:57:11ZPR:Tom10.99962676structure_elementcleaner02023-07-20T14:57:58ZSO:GAT0.9995364evidencecleaner02023-07-20T14:57:22ZDUMMY:structure0.9989391evidencecleaner02023-07-20T15:06:36ZDUMMY:structures0.9998318proteincleaner02023-07-20T14:57:16ZPR:Tollip0.9995357protein_statecleaner02023-07-20T14:58:41ZDUMMY:TBD-0.9995535protein_statecleaner02023-07-20T14:58:47ZDUMMY:ubiquitin-boundTABLEtitle_1730Specifications tablet0010.xmlt0010TABLEtable<?xml version="1.0" encoding="UTF-8"?>
<table frame="hsides" rules="groups"><tbody><tr><td>Subject area</td><td><italic>Biology</italic></td></tr><tr><td>More specific subject area</td><td><italic>Structural biology</italic></td></tr><tr><td>Type of data</td><td><italic>Table, text file, graph, figures</italic></td></tr><tr><td>How data was acquired</td><td><italic>Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz</italic></td></tr><tr><td>Data format</td><td><italic>PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol</italic></td></tr><tr><td>Experimental factors</td><td><italic>Recombinant human Tom1 GAT domain was purified to homogeneity before use</italic></td></tr><tr><td>Experimental features</td><td><italic>Solution structure of Tom1 GAT was determined from NMR chemical shift data</italic></td></tr><tr><td>Data source location</td><td><italic>Virginia and Colorado, United States.</italic></td></tr><tr><td>Data accessibility</td><td><italic>Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d</italic></td></tr></tbody></table>
751Table t0010.xmlt0010TABLEtable<?xml version="1.0" encoding="UTF-8"?>
<table frame="hsides" rules="groups"><tbody><tr><td>Subject area</td><td><italic>Biology</italic></td></tr><tr><td>More specific subject area</td><td><italic>Structural biology</italic></td></tr><tr><td>Type of data</td><td><italic>Table, text file, graph, figures</italic></td></tr><tr><td>How data was acquired</td><td><italic>Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz</italic></td></tr><tr><td>Data format</td><td><italic>PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol</italic></td></tr><tr><td>Experimental factors</td><td><italic>Recombinant human Tom1 GAT domain was purified to homogeneity before use</italic></td></tr><tr><td>Experimental features</td><td><italic>Solution structure of Tom1 GAT was determined from NMR chemical shift data</italic></td></tr><tr><td>Data source location</td><td><italic>Virginia and Colorado, United States.</italic></td></tr><tr><td>Data accessibility</td><td><italic>Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d</italic></td></tr></tbody></table>
760Subject area Biology More specific subject area Structural biology Type of data Table, text file, graph, figures How data was acquired Circular dichroism and NMR. NMR data was recorded using a Bruker 800 MHz Data format PDB format text file. Analyzed by CS-Rosetta, Protein Structure Validation Server (PSVS), NMRPipe, NMRDraw, and PyMol Experimental factors Recombinant human Tom1 GAT domain was purified to homogeneity before use Experimental features Solution structure of Tom1 GAT was determined from NMR chemical shift data Data source location Virginia and Colorado, United States. Data accessibility Data is available within this article. Tom1 GAT structural data is publicly available in the RCSB Protein Data Bank (http://www.rscb.org/) under the accession number PDB: 2n9d 0.99951756experimental_methodcleaner02023-07-20T14:59:18ZMESH:Circular dichroism0.9996252experimental_methodcleaner02023-07-20T14:59:32ZMESH:NMR0.99964654experimental_methodcleaner02023-07-20T14:59:32ZMESH:NMR0.9992082experimental_methodcleaner02023-07-20T15:06:30ZMESH:CS-Rosetta0.9445149experimental_methodcleaner02023-07-20T14:59:43ZMESH:Protein Structure Validation Serverexperimental_methodMESH:cleaner02023-07-20T14:59:52ZPSVS0.97021425experimental_methodcleaner02023-07-20T15:00:05ZMESH:NMRPipe0.9534222experimental_methodcleaner02023-07-20T15:00:07ZMESH:NMRDraw0.99847716speciescleaner02023-07-20T15:00:38ZMESH:human0.9998481proteincleaner02023-07-20T14:57:11ZPR:Tom10.5058204structure_elementcleaner02023-07-20T14:57:58ZSO:GAT0.99844825evidencecleaner02023-07-20T15:00:14ZDUMMY:Solution structure0.99984014proteincleaner02023-07-20T14:57:12ZPR:Tom10.98831964structure_elementcleaner02023-07-20T14:57:58ZSO:GAT0.9996598experimental_methodcleaner02023-07-20T14:59:32ZMESH:NMRevidenceDUMMY:cleaner02023-07-20T15:00:28Zchemical shiftproteinPR:cleaner02023-07-20T14:57:12ZTom1structure_elementSO:cleaner02023-07-20T14:57:58ZGATTABLEtitle_11563Value of the dataTABLEparagraph1581The Tom1 GAT domain solution structure will provide additional tools for modulating its biological function.0.99983656proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.9995917evidencecleaner02023-07-20T15:00:14ZDUMMY:solution structureTABLEparagraph1690Tom1 GAT can adopt distinct conformations upon ligand binding.0.999843proteincleaner02023-07-20T14:57:12ZPR:Tom10.9992766structure_elementcleaner02023-07-20T14:57:58ZSO:GATTABLEparagraph1753A conformational response of the Tom1 GAT domain upon Tollip TBD binding can serve as an example to explain mutually exclusive ligand binding events.0.99981683proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.9990669proteincleaner02023-07-20T14:57:16ZPR:Tollip0.99973947structure_elementcleaner02023-07-20T14:57:36ZSO:TBDTABLEtitle_11903DataTABLEparagraph1908Analysis of the far-UV circular dichroism (CD) spectrum of the Tom 1 GAT domain (Fig. 1) predicts 58.7% α-helix, 3% β-strand, 15.5% turn, and 22.8% disordered regions. The Tom1 GAT structural restraints yielded ten helical structures (Fig. 2A,B) with a root mean square deviation (RMSD) of 0.9 Å for backbone and 1.3 Å for all heavy atoms (Table 1) and estimated the presence of three helices spanning residues Q216-E240 (α-helix 1), P248-Q274 (α-helix 2), and E278-T306 (α-helix 3). Unlike ubiquitin binding, data suggest that conformational changes of the Tom1 GAT α-helices 1 and 2 occur upon Tollip TBD binding (Fig. 3A,B).0.99765813experimental_methodcleaner02023-07-20T15:01:25ZMESH:far-UV circular dichroism0.97389156experimental_methodcleaner02023-07-20T15:01:22ZMESH:CD0.9930906evidencecleaner02023-07-20T15:01:19ZDUMMY:spectrum0.99947125proteincleaner02023-07-20T15:06:22ZPR:Tom 1structure_elementSO:cleaner02023-07-20T14:57:58ZGAT0.999609structure_elementcleaner02023-07-20T15:01:58ZSO:α-helix0.9994879structure_elementcleaner02023-07-20T15:01:59ZSO:β-strand0.99985206proteincleaner02023-07-20T14:57:12ZPR:Tom10.7947963structure_elementcleaner02023-07-20T14:57:58ZSO:GAT0.9988989evidencecleaner02023-07-20T15:06:41ZDUMMY:structural restraints0.9295965evidencecleaner02023-07-20T15:06:45ZDUMMY:structures0.9993277evidencecleaner02023-07-20T15:01:33ZDUMMY:root mean square deviation0.9996222evidencecleaner02023-07-20T15:01:36ZDUMMY:RMSD0.9990892residue_rangecleaner02023-07-20T15:01:42ZDUMMY:Q216-E2400.9997021structure_elementcleaner02023-07-20T15:01:49ZSO:α-helix 10.9991074residue_rangecleaner02023-07-20T15:01:44ZDUMMY:P248-Q2740.9997027structure_elementcleaner02023-07-20T15:01:51ZSO:α-helix 20.99909496residue_rangecleaner02023-07-20T15:01:46ZDUMMY:E278-T3060.99970627structure_elementcleaner02023-07-20T15:01:53ZSO:α-helix 30.99831545chemicalcleaner02023-07-20T15:07:05ZCHEBI:ubiquitin0.99984026proteincleaner02023-07-20T14:57:12ZPR:Tom10.99932325structure_elementcleaner02023-07-20T14:57:58ZSO:GAT0.9996645structure_elementcleaner02023-07-20T15:01:56ZSO:α-helices 1 and 20.9998336proteincleaner02023-07-20T14:57:16ZPR:Tollip0.9960354structure_elementcleaner02023-07-20T14:57:36ZSO:TBDMETHODStitle_12559Experimental design, materials, and methodsMETHODStitle_22603Protein expression and purificationMETHODSparagraph2639Human Tom1 GAT (residues 215–309) cDNA was cloned into both pGEX6P1 and pET28a vectors, and expressed as GST-tagged and His-tagged fusion proteins, respectively, using Escherichia coli [Rosetta (DE3) strain]. The 13C, 15N-labeled Tom1 GAT domain was expressed and purified as described previously.METHODStitle_22939Circular dichroismMETHODSparagraph2958Far-UV CD spectra of the His-Tom1 GAT domain were collected on a Jasco J-815 spectropolarimeter using a 1 mm path length quartz cell at room temperature. The protein (10 μM) was solubilized in 5 mM Tris–HCl (pH 7) and 100 mM KF. Spectra were obtained from five accumulated scans from 190 to 260 nm using a bandwidth of 1 nm and a response time of 1 s at a scan speed of 20 nm/min. Buffer backgrounds were employed to subtract the protein spectra. Data was processed using the Dichroweb server and the CONTIN algorithm (http://dichroweb.cryst.bbk.ac.uk/html/home.shtml).METHODStitle_23539NMR structure determinationMETHODSparagraph3567NMR experiments were performed using 1 mM 13C, 15N-labeled Tom1 GAT domain in a buffer containing 20 mM d11-TrisHCl (pH 7), 50 mM KCl, 1 mM d18-DTT, and 1 mM NaN3. NMR spectra were recorded at 25 °C on a Bruker 800-MHz spectrometer (University of Virginia). The individual structure of Tom1 GAT was generated using CS-Rosetta (https://csrosetta.bmrb.wisc.edu/csrosetta). Chemical shift information (BMRB #26574) was used to obtain the structure calculation. The Rosetta calculations yielded 3000 structures of Tom1 GAT. From these, ten structures were selected based on their score and RMSDs, and converted to Protein Data Bank (PDB) format. NMR structural statistics for the ten lowest energy conformers of Tom1 GAT was generated using the Protein Structure Validation Suite. By using MolProbity, the Ramachandran analysis of the ten superimposed Tom1 GAT structures identified that 100% of the residues were in the most favored regions and there were no Ramachandran outliers in the allowed and disallowed regions. Protein structure images were obtained using PyMol (http://www.pymol.org). The structures of the ubiquitin- and Tollip TBD-bound states of the Tom1 GAT domain were obtained from data reported in Refs. and.REFtitle4797References19101920surname:Xiao;given-names:S.surname:Brannon;given-names:M.K.surname:Zhao;given-names:X.surname:Fread;given-names:K.I.surname:Ellena;given-names:J.F.surname:Bushweller;given-names:J.H.surname:Finkielstein;given-names:C.V.surname:Armstrong;given-names:G.S.surname:Capelluto;given-names:D.G.REFStructureref2320154808Tom1 modulates binding of Tollip to phosphatidylinositol 3-phosphate via a coupled folding and binding mechanism53855391surname:Akutsu;given-names:M.surname:Kawasaki;given-names:M.surname:Katoh;given-names:Y.surname:Shiba;given-names:T.surname:Yamaguchi;given-names:Y.surname:Kato;given-names:R.surname:Kato;given-names:K.surname:Nakayama;given-names:K.surname:Wakatsuki;given-names:S.16199040REFFEBS Lett.ref57920054921Structural basis for recognition of ubiquitinated cargo by Tom1-GAT domainSUPPLtitle_14996Supplementary materialSUPPLfootnote5019Supplementary data associated with this article can be found in the online version at doi:10.1016/j.dib.2016.02.042.gr1.jpgf0005FIGfig_caption5136Representative far-UV CD spectrum of the His-Tom1 GAT domain.0.99858experimental_methodcleaner02023-07-20T15:03:56ZMESH:far-UV CD0.71714723evidencecleaner02023-07-20T15:06:50ZDUMMY:spectrum0.8865229experimental_methodcleaner02023-07-20T15:04:25ZMESH:His-0.9922563proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGATgr1.jpgf0005FIGfig5198Fig. 1.gr2.jpgf0010FIGfig_caption5206(A) Stereo view displaying the best-fit backbone superposition of the refined structures for the Tom1 GAT domain. Helices are shown in orange, whereas loops are colored in green. (B) Ribbon illustration of the Tom1 GAT domain.0.9992467experimental_methodcleaner02023-07-20T15:04:41ZMESH:backbone superposition0.9941738evidencecleaner02023-07-20T15:06:54ZDUMMY:structures0.9998486proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGAT0.99984694proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGATgr2.jpgf0010FIGfig5433Fig. 2.gr3.jpgf0015FIGfig_caption5441(A) Two views of the superimposed structures of the Tom1 GAT domain in the free state (gray) with that in the Tollip TBD-bound state (red). (B) Two views of the superimposed structures of the Tom1 GAT domain (gray) with that in the Ub-bound state (green).0.9534955experimental_methodcleaner02023-07-20T15:05:10ZMESH:superimposed structures0.99984646proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGAT0.99965954protein_statecleaner02023-07-20T15:05:18ZDUMMY:free0.9996728proteincleaner02023-07-20T14:57:16ZPR:Tollip0.99953216protein_statecleaner02023-07-20T15:05:15ZDUMMY:TBD-bound0.9632287experimental_methodcleaner02023-07-20T15:05:12ZMESH:superimposed structures0.9998419proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGAT0.9995443protein_statecleaner02023-07-20T15:05:16ZDUMMY:Ub-boundgr3.jpgf0015FIGfig5697Fig. 3.t0005.xmlt0005TABLEtable_caption5705NMR and refinement statistics for the Tom1 GAT domain. NMR structural statistics for lowest energy conformers of Tom1 GAT using PSVS.0.99963295experimental_methodcleaner02023-07-20T14:59:32ZMESH:NMR0.9961254evidencecleaner02023-07-20T15:05:29ZDUMMY:refinement statistics0.9998447proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGAT0.999608experimental_methodcleaner02023-07-20T14:59:32ZMESH:NMR0.9994303evidencecleaner02023-07-20T15:05:33ZDUMMY:structural statistics0.99985063proteincleaner02023-07-20T14:57:12ZPR:Tom10.9986708structure_elementcleaner02023-07-20T14:57:59ZSO:GAT0.9996277experimental_methodcleaner02023-07-20T15:05:31ZMESH:PSVSt0005.xmlt0005TABLEtable<?xml version="1.0" encoding="UTF-8"?>
<table frame="hsides" rules="groups"><thead><tr><th/><th><bold>Tom1 GAT</bold></th></tr></thead><tbody><tr><td><bold>NMR distance and dihedral constraints</bold></td><td/></tr><tr><td> Dihedral angle restraints total</td><td>178</td></tr><tr><td><italic> ϕ</italic></td><td>89</td></tr><tr><td><italic> ψ</italic></td><td>89</td></tr><tr><td><bold>Structure statistics</bold></td><td/></tr><tr><td> Dihedral angle constraints (deg)</td><td>8.8±0.2</td></tr><tr><td> Max. dihedral angle violation (deg)</td><td>111±3</td></tr><tr><td>Deviations from idealized geometry</td><td/></tr><tr><td> Bond lengths (Å)</td><td>0.011</td></tr><tr><td> Bond angles (deg)</td><td>0.7</td></tr><tr><td>Average pairwise r.m.s. deviation (Å)<xref rid="tbl1fna" ref-type="table-fn">a</xref></td><td/></tr><tr><td> Protein</td><td/></tr><tr><td> Heavy</td><td>1.3</td></tr><tr><td> Backbone</td><td>0.9</td></tr></tbody></table>
5839Table 1. t0005.xmlt0005TABLEtable<?xml version="1.0" encoding="UTF-8"?>
<table frame="hsides" rules="groups"><thead><tr><th/><th><bold>Tom1 GAT</bold></th></tr></thead><tbody><tr><td><bold>NMR distance and dihedral constraints</bold></td><td/></tr><tr><td> Dihedral angle restraints total</td><td>178</td></tr><tr><td><italic> ϕ</italic></td><td>89</td></tr><tr><td><italic> ψ</italic></td><td>89</td></tr><tr><td><bold>Structure statistics</bold></td><td/></tr><tr><td> Dihedral angle constraints (deg)</td><td>8.8±0.2</td></tr><tr><td> Max. dihedral angle violation (deg)</td><td>111±3</td></tr><tr><td>Deviations from idealized geometry</td><td/></tr><tr><td> Bond lengths (Å)</td><td>0.011</td></tr><tr><td> Bond angles (deg)</td><td>0.7</td></tr><tr><td>Average pairwise r.m.s. deviation (Å)<xref rid="tbl1fna" ref-type="table-fn">a</xref></td><td/></tr><tr><td> Protein</td><td/></tr><tr><td> Heavy</td><td>1.3</td></tr><tr><td> Backbone</td><td>0.9</td></tr></tbody></table>
5851 Tom1 GAT NMR distance and dihedral constraints Dihedral angle restraints total 178 ϕ 89 ψ 89 Structure statistics Dihedral angle constraints (deg) 8.8±0.2 Max. dihedral angle violation (deg) 111±3 Deviations from idealized geometry Bond lengths (Å) 0.011 Bond angles (deg) 0.7 Average pairwise r.m.s. deviation (Å)a Protein Heavy 1.3 Backbone 0.9 t0005.xmlt0005TABLEtable_footnote6261Pairwise backbone and heavy-atom r.m.s. deviations were obtained by superimposing residues 215–309 of Tom1 GAT among 10 lowest energy refined structures.0.9994108evidencecleaner02023-07-20T15:05:50ZDUMMY:r.m.s. deviations0.99964523experimental_methodcleaner02023-07-20T15:05:52ZMESH:superimposing0.9990513residue_rangecleaner02023-07-20T15:05:56ZDUMMY:215–3090.99986255proteincleaner02023-07-20T14:57:12ZPR:Tom1structure_elementSO:cleaner02023-07-20T14:57:59ZGAT0.9991259evidencecleaner02023-07-20T15:06:59ZDUMMY:structures