LiteFold/DisProt huggingface dataset:
Protein: DP00324 (UniProt P09651)
Region: residues 183	to 190
Annotation: DNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Third, the region near the carboxyl terminus of UP1 (Lys-183–Ser-190), which was disordered in the absence of DNA, also becomes ordered in the presence of DNA and forms an α-helix (Fig. 2A).
The segment including residues 183–190 was disordered in the protein-only structure, but becomes ordered and forms an α-helix when bound to DNA. The amide group of Lys-183 makes a hydrogen bond with Gua-11, and its side chain interacts with the DNA backbone via a water-mediated interaction. Met-186 makes a van der Waals contact with Ade-9, such that the adenine ring is sandwiched between Met-186 and Phe-108.
Cross-references: PDB:2UP1
Protein: DP00324 (UniProt P09651)
Region: residues 342	to 357
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is missing in the crystal structure but it was not mentioned in the article.
Cross-references: PDB:2H4M
Protein: DP00324 (UniProt P09651)
Region: residues 182	to 186
Annotation: ubiquitination display site (Disorder function)
Evidence: ubiquitination assay evidence used in manual assertion
Supporting statements:
Only mutation of Lys183 among the three lysines (Lys166, Lys179 and Lys183) between amino acid residues 161 and 185 resulted in a decreased level of hnRNP A1 ubiquitylation (Supplementary information, Figure S3D).
Protein: DP00324 (UniProt P09651)
Region: residues 93	to 97
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
IP-western blot revealed that hnRNP-A1 phosphorylation at SQ/TQ motifs was reduced in S95A and S192A single mutant hnRNP-A1 and was eliminated in S95A/S192A double mutant hnRNP-A1 as compared to wild-type hnRNP-A1 (Figure 1C). These results confirm that Ser95 and Ser192 are main phosphorylation residues of hnRNP-A1 and that hnRNP-A1 is phosphorylated by DNA-PKcs in vivo (13,21).
Protein: DP00329 (UniProt P02666)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
at all temperatures and
hydration conditions, the quasielastic intensity of CAS is higher
than that in GFP, suggesting that the IDP shows higher
flexibility and enhanced picosecond dynamics relative to the
rigid β-barrel
Protein: DP00329 (UniProt P02666)
Region: residues 1	to 224
Annotation: disorder to molten globule (Structural transition)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
We show that CAS partially folds and stiffens upon calcium binding, but in the unfolded state, it is softer than folded proteins such as green fluorescence protein (GFP).
Protein: DP00329 (UniProt P02666)
Region: residues 1	to 224
Annotation: calcium ion binding (Molecular function)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
An IDP, β-casein
(CAS), has been studied in a calcium bound and unbound
state using neutron and light scattering techniques.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The purified proteins were concentrated to 15 mg/ml and subjected to standard one dimensional proton NMR.
The narrow spread of the peptide backbone amide NH peaks (7.8–8.6 ppm) and the side chain NH peaks (6.6–7.4 ppm) are indicative of a lack of ordered structures over the NMR time scale.
Therefore, both BSP and OPN, when purified and isolated in solution, are flexible along their entire length and have no significant regions that persist in a single structural environment for more than a few milliseconds.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: small molecule binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
For example, we have shown previously that BSP can bind strongly to hydroxyapatite (HA) and does so throughout most of its entire length. For BSP to function as an attachment protein for cells to attach to HA (as has been frequently proposed by people in the bone field), the BSP would be bound to HA along its length and yet keep its RGD domain available to bind an integrin such as aVb3.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: protein binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
BSP can also bind first to the alpha-V/beta-3 integrin then it can bind to complement
Factor H (Fig. 3A). This four-subunit complex stops the lytic pathway of complement in vitro (10). If, however, Factor H binds to BSP before the latter can bind to its integrin, the Factor H binds throughout the length of BSP blocking its ability to subsequently bind to the integrin. The integrin-binding domain of BSP can therefore bind to either the integrin or to specific portions of Factor H.
Protein: DP00332 (UniProt P21815)
Region: residues 285	to 289
Annotation: protein binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
RGD domain available to bind an integrin such as alpha-V/beta-3
Protein: DP00332 (UniProt P21815)
Region: residues 285	to 289
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
 Furthermore, preincubation of MEL cells with either GRGDS peptide or an aVb3 antibody (which blocks that integrins binding activity) negated the protective effect of rBSP.
Protein: DP00332 (UniProt P21815)
Region: residues 285	to 289
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Preincubation  of  MEL  cells  with  rBSP whose  RGD  sequence  had  been  mutated  to  KAE  completely removed the protective affects of this protein.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
By steady state fluorescence, the binding of BSP  and  OPN  by  Factor  H  are  saturable  and  possess  a  1:1 stoichiometry, have binding constants in the nanomolar range, given the serum concentration of Factor H (0.5 mg/ml), virtually all BSP and OPN in serum will be complexed with Factor H.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: small molecule binding (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
BSP has long been known to have an affinity for hydroxyapatite. A UMR-BSP hydroxyapaptite dissociation constant of 2.6 3 1029 M was calculated utilizing a molecular weight of 67.9 kD and a modification of the Scatchard method.
Protein: DP00332 (UniProt P21815)
Region: residues 258	to 317
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A 59 amino acid recombinant RGD domain was produced in minimal media using 15NH4Cl as the sole source of nutrient nitrogen. The HSQC two-dimensional
NMR spectrum showed a narrow spread of chemical shifts characteristic of a flexible structure or “random coil.”
Protein: DP00332 (UniProt P21815)
Region: residues 258	to 317
Annotation: protein binding (Molecular function)
Evidence: adhesion assay evidence used in manual assertion
Supporting statements:
However, unlike the other recombinant BSP proteins, both the normal 258E–317Q
(RGD) protein and the mutant 258E–317Q (KAE) protein mediated cell attachment were affected by the addition of GRGDS peptide.
It is clear from the authors' description that with this mutation they tested the integrin binding ability. While the whole protein retained cell attachment ability in the presence of the mutations (it also has another, integrin-independent attachment site), the cell attachment ability of the C-terminal segment was sensitive for the presence of competeing RGD-containing peptides.
Protein: DP00332 (UniProt P21815)
Region: residues 1	to 317
Annotation: molecular adaptor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Thus, BSP is a protein that can be bound along most of its length separately to at least two different binding partners in vivo. The simplest way to do this is to have a completely unstructured protein essentially alternating sequences that can specifically interact with the different binding partners.
BSP can also bind first to the avb3 integrin then it can bind to complement Factor H. This four-subunit complex stops the lytic pathway of complement in vitro.
Protein: DP00333 (UniProt P27797)
Region: residues 367	to 417
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Results revealed a MW of 40 634 Da which based on the sequence of human CRT (and thepresence of four additional amino acid residues at the N-terminus, see Experimental Procedures) can be most closely correlated with the cleavage of 51 residues from the C-terminus of the protein. Collectively, these findings are entirely consistent with the presence of a region at the C-terminus of CRT in which the polypeptide backbone is most exposed and conformationally flexible in solution andtherefore more susceptible to proteolysis by thermolysin.
Protein: DP00333 (UniProt P27797)
Region: residues 367	to 417
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Results revealed a MW of 40 634 Da which based on the sequence of human CRT (and thepresence of four additional amino acid residues at the N-terminus, see Experimental Procedures) can be most closely correlated with the cleavage of 51 residues from the C-terminus of the protein. Collectively, these findings are entirely consistent with the presence of a region at the C-terminus of CRT in which the polypeptide backbone is most exposed and conformationally flexible in solution andtherefore more susceptible to proteolysis by thermolysin.
Protein: DP00333 (UniProt P27797)
Region: residues 18	to 417
Annotation: molten globule (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
These calculations yielded a value of f / f0) 1.65 using a partial specific volume of 0.695 cm3/g and hydration of 0.502 g of H2O/g of protein. Using these values, CRT could be  represented  as  a  prolate  of  ellipsoid  of  revolution  with an apparent axial ratio of 12.2, having a length of 29.8 nm and a diameter of 2.44 nm (Table 1). Based on this model, the  hydrodynamic  dimensions  clearly  indicate  that  monomeric CRT is an asymmetric elongated molecule in solution.
The distinctively  nonspherical  shape  of  CRT  is consistent  with  secondary  structure  predictions  suggesting that  certain  regions  of  the  protein  are  likely  to  adopt  an extended conformation in solution ( 17, 44 ).
Sedimentation equilibrium and velocity experiments clearly established  that  this  anomalous  behavior  arises  from  the highly elongated shape of monomeric CRT.
Protein: DP00333 (UniProt P27797)
Region: residues 18	to 307
Annotation: order (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
This analysis reveals that proteolytic fragments corresponding to bands 1 and 2 share a common core region  that  includes  most  of  the  N-domain  (residues  60 180) and a major portion of the P-domain (residues 180  226), emphasizing that this region of the protein adopts a stable  and  rigid  three-dimensional  structure  in  solution.
N-domain of CRT is likely to fold into a globular structure within the protein   (17,   44),   thus conferring increased protection against proteolysis. The single site of thermolytic cleavage identified in the  N-domain  is  at  position  Leu  60(Table  2)  and is likely  to be  located  in  a  more  surface-exposed region, such as a loop or a turn, within the spatial arrangement of this domain.
The analysis presented in Figure 6 also indicates that band3 corresponds to the P-domain of CRT and encompasses the type 1 and type 2 sequence motifs (17, 44) which have been suggested to be important for the lectin function of CRT (7,18). The presence of this fragment in the proteolytic mixture provides  evidence  that  isolated  domains  of  CRT  can  be independently  stable  in  solution
Collectively, these studies provide experimental evidence that support  and  extend  the  early  structural  characterization  of CRT which predicted from secondary structure analysis that the general shape of the protein is a large globular N-terminus region  followed  by  a  more  elongated  C-terminal  region ( 17, 44 ).
Protein: DP00333 (UniProt P27797)
Region: residues 308	to 417
Annotation: molten globule (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Results (Table 2) indicate that two of the fragments (bands 1 and 2) are characterized by extensive loss of residues at the C-terminus of the protein but more limited cleavage at the  N-terminus
This observation suggests that the C-domain may be an important determinant in  initiating  the  thermal  denaturation  of  CRT  and  also  supports the view that this domain is likely to adopt a more loosely  packed  conformation  in  solution  ( 17,  44 ).  Collectively, these studies provide experimental evidence that support  and  extend  the  early  structural  characterization  of CRT which predicted from secondary structure analysis that the general shape of the protein is a large globular N-terminus region  followed  by  a  more  elongated  C-terminal  region ( 17, 44 ). 
Interestingly,  results  from Figure 5 (lane at 50°C) indicate that fragments lacking the C-domain   (e.g.,   bands   1-3)   exhibit   increased   thermals tability in comparison to full-length CRT. This observation suggests that the C-domain may be an important determinant in  initiating  the  thermal  denaturation  of  CRT  and  also supports the view that this domain is likely to adopt a moreloosely  packed  conformation  in  solution
Protein: DP00333 (UniProt P27797)
Region: residues 18	to 417
Annotation: molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Based on its elution position corresponding to that of a globular protein of MW 158 kDa (Figure 1A), the Stokes radius of CRT was calculated to be 46.2 Å (see Experimental Procedures). This value is considerably larger than the calculated value of 29.4 Å assuming CRT to be a monomeric globular protein in solution (see Experimental Procedures). The experimentally determined Stokes radius of 46.2 Å is, however, significantly different from the calculated value of 64.2 Å assuming CRT to be completely unfolded in solution
Consequently, the apparent large size of CRT determined on the gel filtration column is more likely to be accounted for on the basis of its intrinsic molecular properties such as the presence of partly denatured regions, a welldefined oligomeric state in solution, an asymmetric shape, or a combination of these factors.
Our results from gel filtration chromatography indicate that CRT elutes at a position corresponding to a significantly larger size based on calibration of the column using globular protein standards.
Protein: DP00333 (UniProt P27797)
Region: residues 18	to 417
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Taken together, the CD analysis suggests that although the three-dimensional structure of CRT is overall characterized by well-packed side chains, as evidenced by the pronounced near-UV CD spectrum and the cooperative nature of the thermal denaturation transitions, the relatively low Tm values suggest a marginally stable core structure.
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: selective autophagy (Biological process)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
LIR motifs of known autophagy receptors and adaptors feature mATG8 specificity.
A high number of autophagy receptors or adaptor structures have been reported, yet the basis for their selective interaction with individual members of the ATG8 family is not well understood. We speculated whether the LIR motif alone is able to confer selectivity towards a mATG8 subfamily and whether we could derive a subfamily consensus motif from analysis of known mATG8 interaction partners. To address this question, we screened an array of peptides (presented in Fig EV1A and described in Materials and Methods) with the LIR sequences of 30 known and validated autophagy receptors and adaptors (Table 1) against all six human mATG8s for binding (Figs 1A and EV1B and C). In brief, biotinylated peptides were immobilized on streptavidin‐coated 96‐well plates and incubated with His6‐tagged mATG8 proteins. After washing steps, peptide‐bound mATG8 was detected in an ELISA reader using anti‐His antibodies directly conjugated to HRP (horse radish peroxidase; Fig EV1A).
The annotated region include the LIR motif (WDFL) at position 200-203.
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: protein binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
LIR motifs of known autophagy receptors and adaptors feature mATG8 specificity.
A high number of autophagy receptors or adaptor structures have been reported, yet the basis for their selective interaction with individual members of the ATG8 family is not well understood. We speculated whether the LIR motif alone is able to confer selectivity towards a mATG8 subfamily and whether we could derive a subfamily consensus motif from analysis of known mATG8 interaction partners. To address this question, we screened an array of peptides (presented in Fig EV1A and described in Materials and Methods) with the LIR sequences of 30 known and validated autophagy receptors and adaptors (Table 1) against all six human mATG8s for binding (Figs 1A and EV1B and C). In brief, biotinylated peptides were immobilized on streptavidin‐coated 96‐well plates and incubated with His6‐tagged mATG8 proteins. After washing steps, peptide‐bound mATG8 was detected in an ELISA reader using anti‐His antibodies directly conjugated to HRP (horse radish peroxidase; Fig EV1A).
The annotated region include the LIR motif (WDFL) at position 200-203.
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: protein binding (Molecular function)
Evidence: immunocytochemistry evidence used in manual assertion
Supporting statements:
Immunocytochemical localization studies in fixed NEURO-2a (N2a) cells showed that both proteins partially colocalize, or at least are not visibly separated, in different cellular compartments (Fig. 6). In addition to the reported cytosolic appearance of both GABARAP and CRT [[4, 18]], these results indicate the possibility for direct interaction.
Figure 6 Localization of GABARAP and CRT in fixed N2a cells. (A) Differential interference contrast image of N2a cells. (B) Immunofluorescence of Alexa488-labelled anti-GABARAP serum in green. (C) Immunofluorescence of Alexa647-labelled anti-CRT serum in red. (D) Merging of (B) and (C).
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Immunocytochemical localization studies in fixed NEURO-2a (N2a) cells showed that both proteins partially colocalize, or at least are not visibly separated, in different cellular compartments (Fig. 6). In addition to the reported cytosolic appearance of both GABARAP and CRT [[4, 18]], these results indicate the possibility for direct interaction.
Figure 6 Localization of GABARAP and CRT in fixed N2a cells. (A) Differential interference contrast image of N2a cells. (B) Immunofluorescence of Alexa488-labelled anti-GABARAP serum in green. (C) Immunofluorescence of Alexa647-labelled anti-CRT serum in red. (D) Merging of (B) and (C).
Indeed, Sepharose-immobilized GABARAP was found to interact with endogenous CRT from brain extracts (Fig. 7A). By contrast, Sepharose without immobilized GABARAP, but otherwise identically treated, did not show CRT immunoreactivity.
Figure 7 GABARAP associates with CRT. (A) Endogenous CRT binds to immobilized GABARAP. Control Sepharose alone (lane 2) and Sepharose-coupled GABARAP in the presence (lane 3) and absence (lane 4) of 1150 µm N1 were exposed to rat brain extracts. After extensive washing, bound material was resolved by SDS-PAGE and analysed by immunoblotting with anti-CRT serum. Control Sepharose (lane 2) shows no indication for binding, whereas Sepharose-coupled GABARAP exhibits immunoreactivity for CRT. Only very weak immunoreactivity was observed in the presence of N1 peptide (lane 4). For convenience, lane 1 shows the bands of a prestained protein marker (Prestained Protein Marker, Broad Range, NEB, Beverly, MA, USA). (B) Endogenous GABARAP binds to immobilized CRT. Control Sepharose (lane 2) and Sepharose-coupled CRT were exposed to rat brain extracts. After extensive washing, bound material was resolved by SDS-PAGE and analysed by immunoblotting with anti-GABARAP serum. Two signals with GABARAP immunoreactivity are clearly visible.
The interaction of CRT and GABARAP was further confirmed by a pull-down experiment of endogenous GABARAP with recombinant CRT immobilized on NHS-activated Sepharose (CRT-Sepharose). CRT-Sepharose was exposed to rat brain extracts, and CRT-Sepharose-associated proteins were separated by SDS-PAGE and probed by western blot analysis for GABARAP immunoreactivity. Sepharose-immobilized CRT was found to interact with endogenous GABARAP from brain extracts (Fig. 7B).
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
SPR was used to investigate quantitatively the interaction of recombinant GABARAP with recombinant CRT. GABARAP was immobilized on a CM5 sensor chip using standard amine coupling procedures. The injection of CRT on the sensor chip resulted in binding to GABARAP, as indicated by an injection time-dependent increase in the SPR response. Dissociation of bound CRT from the sensor chip was very slow, indicating a very low dissociation rate of CRT from GABARAP. Apart from a small change in the bulk refractive index during injection, no interaction of CRT with the reference surface was observed.
Protein: DP00333 (UniProt P27797)
Region: residues 199	to 204
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
1H–15N correlation NMR (heteronuclear single quantum correlation, HSQC) spectra of GABARAP labelled with the stable isotope 15N were recorded during the course of titration with unlabelled CRT. The NMR spectrum of GABARAP without CRT exhibited the known and expected resonances typical for natively folded GABARAP [[22]]. The addition of CRT to GABARAP resulted in the disappearance of GABARAP resonances, a clear indication of binding (Fig. 3B).