LiteFold/DisProt huggingface dataset:
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 25	to 79
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR data clearly indicate that the fairly long N- and C-terminal regions (residues 1-55 and 145-189) of sclerostin are highly flexible and completely disordered (Fig. 2A).
The IDR characterized in the publication residues 1-55 corresponds to region 25-79 of the amino acid sequence.
Cross-references: PDB:2K8P
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 169	to 213
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR data clearly indicate that the fairly long N- and C-terminal regions (residues 1-55 and 145-189) of sclerostin are highly flexible and completely disordered (Fig. 2A).
The IDR characterized in the publication residues 145-189 corresponds to region 169-213 of the amino acid sequence.
Cross-references: PDB:2K8P
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 110	to 133
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In common with the N- and C-terminal regions, loop 2 appears to be relatively flexible and adopts a diverse range of conformations within the family of converged structures.
The loop 2 corresponds to the region 110-133.
Cross-references: PDB:2K8P
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 110	to 133
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Identification of the Binding Site of an Antibody That Antagonizes the Inhibition of Wnt Signaling by Sclerostin
As described for heparin, the location of the inhibitory antibody binding site on sclerostin was mapped by following the changes in the positions of backbone amide NMR signals (15N and 1H) induced by the binding of the Fab fragment of the inhibitory antibody.
Examples of significantly affected amide signals of sclerostin are highlighted in the selected regions of 1H,15N HSQC spectra shown in Fig. 8A. The combined minimal shift values for the backbone amide signals versus protein sequence are shown in the histogram in Fig. 8B, which indicates that the majority of the perturbed residues are located within the flexible and solvent exposed loop 2 region of sclerostin (Fig. 8C).
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 110	to 133
Annotation: carbohydrate binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The predicted binding of heparin to sclerostin was confirmed by detecting changes in the positions of backbone amide NMR signals (15N and 1H) induced by binding of a dodecameric heparin fragment (Fig. 5A). The binding of the heparin fragment clearly results in very significant shifts in the positions of backbone amide signals from residues located mainly in loops 2 and 3, in particular, Glu-53, Ser-55, Arg-57, His-60, Ser-82, Gly-83, Leu-91, Trp-100, Trp-101, Arg-102, Ser-104, Asp-113, Arg-114, Tyr-115, Arg-116, Ala-117, Arg-119, Val-120, Gln-121, Leu-122, Leu-123, Glu-128, Ala-129, Arg-131, Ala-132, Val-135, Leu-137, Val-138, Cys-141, Lys-144, and Leu-146 (Fig. 5B).
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 115	to 121
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To understand the interactions in detail, we determined high-resolution structures of DKK1 and SOST peptides in complex with LRP6 E1.
In the case of the SOST peptide, the Ile is followed by an intervening Gly before the basic Arg residue. This reorients the peptide backbone and places the Arg side chain in a more peripheral location on the acidic patch of LRP6 (Figure 4B).
Cross-references: PDB:3SOV
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 115	to 121
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To understand the interactions in detail, we determined high-resolution structures of DKK1 and SOST peptides in complex with LRP6 E1.
Taken together, the binding data and the effects on Wnt signaling confirm that the conserved “NXI” motif is functionally relevant for DKK1 and SOST inhibition of those Wnts signaling through binding to E1E2, and that the DKK1 CRD2 interaction with E3E4 is important only for inhibition of a different subset of Wnt ligands.
Cross-references: PDB:3SOV
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 115	to 121
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
For wild-type DKK1 and SOST, strong inhibition of WNT1-dependent signaling is observed.
Taken together, the binding data and the effects on Wnt signaling confirm that the conserved “NXI” motif is functionally relevant for DKK1 and SOST inhibition of those Wnts signaling through binding to E1E2, and that the DKK1 CRD2 interaction with E3E4 is important only for inhibition of a different subset of Wnt ligands.
The luciferase repoter assay was used to detect the interaction and DEXA scans measured the total bone marrow density.
Protein: DP00926 (UniProt Q9BQB4)
Region: residues 110	to 133
Annotation: localization (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Heparin Mediates the Localization of Sclerostin at the Cell Surface
 Additions of heparin to the cell culture for 3 h before the harvest of the supernatant resulted in a striking dose-dependent increase in the amount of sclerostin detected in the supernatant without affecting the total amount of sclerostin produced by the cells, as shown in Fig. 6A.
The experimental data reported here clearly indicates that the interaction between heparan sulfate and sclerostin will result in a significantly higher concentration of the protein at the surface of responsive cells, which may facilitate its regulation of the Wnt/β-catenin signaling pathway in a more spatially controlled and temporally dependent manner.
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far UV CD spectra of CcdA37-72 at 25 °C. The spectrum in blue is of unbound CcdA37-72 and has the typical shape of a random coil spectrum.
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far UV CD spectra of CcdA37-72 at 25 °C. The spectrum in blue is of unbound CcdA37-72 and has the typical shape of a random coil spectrum. The spectrum in green is the difference spectrum  between  the  CcdB2:CcdA37-72  complex  and  CcdB2,  thus  corresponding  to  that  of  CcdA37-72 in its bound state. Here the typical spectral shape corresponding to α-helix is clearly visible.
Upon  addition  of  CcdA37-72 to  CcdB2,  the  CD  spectrum  of  CcdA37-72  undergoes  significant  changes.  Figure  S1A  compares  the  far  UV  CD  spectrum  of  CcdA37-72  in  its  free  state  and  in  complex  with  a  CcdB  dimer  (CcdB2:CcdA37-72  ratio  1:1).  The  latter  indicates  that  upon  complex formation CcdA37-72 folds to a largely α-helical conformation, in agreement with our crystallographic studies.
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Upon addition of CcdA37-72 to CcdB2, the CD spectrum of CcdA37-72 undergoes significant changes. Figure S1A compares the far UV CD spectrum of CcdA37-72 in its free state and in complex with a CcdB dimer (CcdB2:CcdA37-72 ratio 1:1).
Binding studies using ITC, SPR, CD-, and fluorescence spectroscopy consistently yield a picture of the CcdB2 dimer possessing two binding sites for CcdA37-72, differing in affinity by a factor of at least 106 (Figure 2 and Figure S4).
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The  fingerprint  region  of  the  TOCSY  spectrum  of  CcdA37-72  shows  poor  chemical  shift  dispersion.   They   all   fall   in   the   range   between   7.8-8.6   ppm,   typical   for   random   coil   conformations
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
The near UV CD spectrum of CcdA37-72 lacks sharp peaks, which is an indication of disorder.
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Fluorescence spectroscopy measurements of CcdA37-72 show a monotonic increase upon chemical unfolding with guanidinium chloride and the absence of a discrete folding/unfolding transition.
Protein: DP00928 (UniProt P62552)
Region: residues 41	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Sequential backbone and side-chain assignments localized the well-dispersed signals to residues 3–40. Values closer to random coil shifts were
observed for the C-terminal 30 residues, together
with three different conformations (labeled “a”, “b” and “c” in Figure 1(b) and (c)). These provide evidence that CcdA consists of two domains, a structured N terminus (CcdAN; Gln3–Arg40) and a much more flexible C terminus (CcdAC; Ala41– Trp72) which adopts different, partially stable conformations.
The CcdA R70K mutant was used in the NMR measurement that showed increased stability against proteolytic cleavage.
Cross-references: PDB:2ADL
PDB:2H3A
PDB:2H3C
PDB:2ADN
Protein: DP00928 (UniProt P62552)
Region: residues 32	to 72
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Purified CcdA41, however, contained almost no α-helical or β-sheet structure.
Protein: DP00928 (UniProt P62552)
Region: residues 32	to 72
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The intrinsic fluorescence of CcdA had an emission maximum at 346 nm, suggesting that both tryptophan residues are highly solvent-exposed (Fig. 8).
Protein: DP00928 (UniProt P62552)
Region: residues 32	to 72
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Changes in CcdA fluorescence also suggest a conformational change in CcdA upon binding CcdB. The intrinsic fluorescence of CcdA41 was similar to that of CcdA and was blue-shifted to a similar extent upon binding of CcdB. The intrinsic fluorescence of CcdA had an emission maximum at 346 nm, suggesting that both tryptophan residues are highly solvent-exposed (Fig. 8). Addition of CcdB results in a dramatic blue shift in the fluorescence emission which had a maximum near 330 nm (Fig. 8), indicating that both tryptophan residues are buried in the complex. The intrinsic fluorescence of CcdA41 was similar to that of CcdA and was blue-shifted to a similar extent upon binding of CcdB (data not shown). Burial of the tryptophan residues could indicate that those residues form part of the bonding domain between CcdA and CcdB or that CcdB binding induces a conformational change in CcdA that moves the tryptophan residues away from the solvent into closer contact with other residues in the terminal a-helix.
Protein: DP00928 (UniProt P62552)
Region: residues 41	to 72
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In solution, CcdA37-72 behaves as a monomeric and intrinsically disordered protein and folds upon binding to CcdB. Electron density is observed for residues Ala41-Trp72, while residues Arg37-Arg40 remain disordered. Segment Arg40-Gly63 forms a long bent α-helix. Segment Ser64-Trp72, on the other hand, has a more irregular structure harboring just a single helical turn at its center.
Cross-references: PDB:3G7Z
PDB:3HPW
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of the CcdB2:CcdA37-72 complex is asymmetric with a single CcdA37-72 domain wrapped around the CcdB2 dimer in a largely α-helical conformation, burying a total combined molecular surface of 2850 Å2 for CcdA37-72 and CcdB2.
Cross-references: PDB:3G7Z
PDB:3HPW
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: toxin sequestering activity (Molecular function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
We found that coexpression with CcdA37-72 is sufficient to protect E. coli cells from CcdB. The
growth of cells cotransformed with plasmids coding for CcdB and CcdA37-72 (efficiency of plating [EOP] = 0.9 ± 0.2) is similar to the growth of cells transformed with plasmids coding for
CcdB and full-length CcdA (EOP = 0.8 ± 0.3). Cells transformed with a plasmid coding only for CcdB produce very few colonies (EOP = 0.002 ± 0.002).
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding studies using ITC, SPR, CD-, and fluorescence spectroscopy consistently yield a picture of the CcdB2 dimer possessing two binding sites for CcdA37-72, differing in affinity by a factor of at least 106 (Figure 2 and Figure S4).
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Binding studies using ITC, SPR, CD-, and fluorescence spectroscopy consistently yield a picture of the CcdB2 dimer possessing two binding sites for CcdA37-72, differing in affinity by a factor of at least 106 (Figure 2 and Figure S4).
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Binding studies using ITC, SPR, CD-, and fluorescence spectroscopy consistently yield a picture of the CcdB2 dimer possessing two binding sites for CcdA37-72, differing in affinity by a factor of at least 106 (Figure 2 and Figure S4).
Protein: DP00928 (UniProt P62552)
Region: residues 37	to 72
Annotation: protein-containing complex disassembly (Biological process)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
In order to determine how many molar equivalents of CcdA37-72 are required to disrupt the GyrA592:CcdB2 complex, we performed a series of analytical gel filtration experiments where GyrA592:CcdB2 was preincubated with different molar equivalents of CcdA37-72. Adding a single equivalent of monomeric CcdA37-72 to GyrA592:CcdB2 fully dissociated this complex, producing GyrA592 and CcdB2:CcdA37-72 (Figure 3C), confirming the functional relevance of our crystal structure. This result directly links the high-affinity interaction between CcdB and CcdA37-72 to the rejuvenation process.
Protein: DP00928 (UniProt P62552)
Region: residues 46	to 71
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To map the regions of CcdA involved in the binding to the toxin CcdB a titration of unlabeled CcdB with increasing amounts of uniformly 13C/15N labeled CcdA was carried out. Significant chemical shift changes were observed for NH resonances of residues located within the C-terminal region of CcdA only (residues between Val46 and Asp71) and addition of CcdB had no effect on the N-terminal domain (Figure 4(a)).
Protein: DP00928 (UniProt P62552)
Region: residues 46	to 72
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The residues located in CcdAC (green peaks; labels written in circles) were unaffected by residual proteases in the CcdB solution which successively digested CcdAN.
We observed that upon binding to CcdB, CcdAC becomes structured and that residues 46 to 72 are shielded in the complex.
Protein: DP00928 (UniProt P62552)
Region: residues 1	to 72
Annotation: protein binding (Molecular function)
Evidence: native protein gel electrophoresis evidence used in manual assertion
Supporting statements:
Complex of CcdA and CcdB—CcdA and CcdB interact to form a stable complex that can be isolated by gel filtration (Fig. 1A) or native gel electrophoresis (Fig. 2, A and C).
Protein: DP00928 (UniProt P62552)
Region: residues 1	to 72
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Complex of CcdA and CcdB—CcdA and CcdB interact to form a stable complex that can be isolated by gel filtration (Fig. 1A) or native gel electrophoresis (Fig. 2, A and C).
Protein: DP00928 (UniProt P62552)
Region: residues 32	to 72
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
CcdA41 was also degraded by Lon, but in this case similar degradation rates were observed with either ATP or AMPPNP.
While full length CcdA could only be degraded by Lon in the presence of ATP, CcdA41 was degraded by Lon independent of the presence of ATP.  This suggests that while full length CcdA has considerable amount of secondary structure, the C-terminal region (CcdA41) has not.
Protein: DP00928 (UniProt P62552)
Region: residues 32	to 72
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
CcdB blocked activation of Lon ATPase activity by CcdA (Table IV), which suggests that CcdA can not interact with Lon when CcdA and CcdB are in a complex. Thus, CcdB protects CcdA probably by masking or making inaccessible those regions of CcdA normally recognized by Lon. CcdB also partially protects CcdA from degradation by proteases such as LysC and V8 protease.
Protein: DP00928 (UniProt P62552)
Region: residues 41	to 72
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Traces of proteases remaining in the CcdB solution digested CcdAN while CcdAC was protected against proteolysis even after weeks at room temperature.
Protein: DP00929 (UniProt P04608)
Region: residues 50	to 86
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Density was not observed for the amino acid residues 1-7, 89-96, 345 and the C-terminal His-tag of Cdk9, for the residues 1-6, 253-260 and 262-266 of Cyclin T1, and for the residues 50-86 of Tat.
Cross-references: PDB:3MI9
PDB:3MIA
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 49
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Indeed, the residues 1-49 are ordered in the crystal structure of Tat•P-TEFb, while the density for the rest of Tat (residues 50-86) is not defined.
This region is ordered when bound to the positive transcription elongation factor, P-TEFb.
Cross-references: PDB:3MI9
PDB:3MIA
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 49
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Indeed, the residues 1-49 are ordered in the crystal structure of Tat•P-TEFb, while the density for the rest of Tat (residues 50-86) is not defined.
This region is ordered when bound to the positive transcription elongation factor, P-TEFb.
Cross-references: PDB:3MI9
PDB:3MIA
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 49
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Indeed, the residues 1-49 are ordered in the crystal structure of Tat•P-TEFb, while the density for the rest of Tat (residues 50-86) is not defined.
Cross-references: PDB:3MI9
PDB:3MIA
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 49
Annotation: molecular sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Indeed, the residues 1-49 are ordered in the crystal structure of Tat•P-TEFb, while the density for the rest of Tat (residues 50-86) is not defined.
Cross-references: PDB:3MI9
PDB:3MIA
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 57
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This region is 100% identical to that of Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Tat protein, proved to be disordered.
Cross-references: DisProt:DP03535
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
In the absence of interacting partners, Tat does not have prominent secondary structure elements, indicating the flexible nature of free Tat proteins.
Protein: DP00929 (UniProt P04608)
Region: residues 62	to 68
Annotation: phosphorylation display site (Disorder function)
Evidence: author statement used in manual assertion
Supporting statements:
The same material was subjected to sequential Edman degradation, and the release of radioactive derivatives was monitored. Peaks of radioactivity were observed at cycles 6, 8, and 12, indicative of phosphorylation sites at these distances following an arginine or lysine residue. The only place that such a pattern occurs in the Tat-72 molecule is at serine 62, threonine 64, and serine 68 (Fig. 5C).
Protein: DP00929 (UniProt P04608)
Region: residues 49	to 72
Annotation: protein binding (Molecular function)
Evidence: protein binding evidence used in manual assertion
Supporting statements:
GST-Tat 86, GST-Tat 72, and their mutant variants, p18IS and C22G, all bound PKR, whereas the 48Δ Tat truncation and its associated mutants failed to bind PKR. In addition the Tat construct Tat 86Δ2/36, an N-terminal deletion of residues 2-36 from GST-Tat 86, successfully bound activated PKR. These data suggest that the Tat sequence contained between amino acids 49 and 72 is important for binding PKR, but the N-terminal and C-terminal residues 2-36 and 73-86 are dispensable.