LiteFold/DisProt huggingface dataset:
Protein: DP01458 (UniProt Q9Y3B4)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The flanking N- (residues 1–
20) and C-terminal regions (residues 100–125) are unstructured.
Protein: DP01459 (UniProt P41352)
Region: residues 427	to 443
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this case, the peak positions were fully consistent with the supposition that the C-terminal tails are
disordered
Protein: DP01460 (UniProt P41351)
Region: residues 431	to 449
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this case, the peak positions were fully consistent with the supposition that the C-terminal tails are disordered
Protein: DP01461 (UniProt Q13188)
Region: residues 314	to 427
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By contrast, the 1H/15N TROSY-HSQC spectrum of the Mst2 mutant with its linker between the kinase and SARAH domains deleted (Mst2ΔL) had few sharp peaks, indicating that the Mst2 linker was natively unfolded (Figure S4B).
Protein: DP01461 (UniProt Q13188)
Region: residues 314	to 427
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By contrast, the 1H/15N TROSY-HSQC spectrum of the Mst2 mutant with its linker between the kinase and SARAH domains deleted (Mst2ΔL) had few sharp peaks, indicating that the Mst2 linker was natively unfolded (Figure S4B).
Protein: DP01461 (UniProt Q13188)
Region: residues 365	to 367
Annotation: selective autophagy (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
STK3 interacts with LC3C and GABARAP via a CLIR
Figure 1. STK3 interacts with LC3C and GABARAP via a C-type atypical LIR motif. E, schematic drawing of the domain organization of STK3 with the kinase domain, the LIR motif, and the SARAH domain indicated. The extent of deletion mutants and the location of the MVI/AAA LIR mutation are shown below the domain cartoon. G, and H, GST pulldown analyses of binding of Myc-tagged STK3 WT and LIR mutant translated in vitro in the presence of [35S]methionine to GST-LC3C (G) or Myc-tagged STK3 WT translated in vitro in the presence of [35S]methionine to GST-LC3C or GST-LC3C F58A (H). The F58A mutant inhibits binding to the LDS of LC3C. I, HEK293 cells were transiently transfected with FLAG-tagged constructs of STK3 WT and LIR mutant (MVI/AAA), and whole-cell lysates were incubated with recombinant GST or GST–ATG8s family proteins. 
However, because STK3 also bound strongly to LC3C, we searched the C-terminal part of STK3 for CLIR with the consensus ΦΦΦ, where Φ is an aliphatic amino acid. 
A candidate CLIR, “MVI” was located at positions 365–367, reminiscent of the CLIR previously described for the interaction between CALCOCO2/NDP52 and LC3C (36).
Strikingly, mutation of this CLIR motif to AAA abolished binding between STK3 and LC3C (Fig. 1G). 
Consistently, mutation of the LDS in LC3C F58A resulted in a strongly-decreased binding to STK3 (Fig. 1H).
GST-pulldown assays using extracts from HeLa cells expressing the FLAG–STK3 or the FLAG–STK3 MVI/AAA CLIR mutant verified the strong binding of FLAG–STK3 to GABARAP and LC3C, whereas the CLIR mutant FLAG–STK3 MVI/AAA did not show significant binding.
Furthermore, the GABARAP Y49A LDS mutant displayed strongly-reduced binding to FLAG–STK3 (Fig. 1I).
Taken together, the results show that the CLIR motif in STK3 mediated LDS-dependent binding to both LC3C and GABARAP.
The annotation include the non canonical CLIR motif MVI at position 365 – 367.
Protein: DP01461 (UniProt Q13188)
Region: residues 365	to 367
Annotation: selective autophagy (Biological process)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
STK3 interacts with LC3C and GABARAP via a CLIR
Figure 1. STK3 interacts with LC3C and GABARAP via a C-type atypical LIR motif. G, and H, GST pulldown analyses of binding of Myc-tagged STK3 WT and LIR mutant translated in vitro in the presence of [35S]methionine to GST-LC3C (G) or Myc-tagged STK3 WT translated in vitro in the presence of [35S]methionine to GST-LC3C or GST-LC3C F58A (H). The F58A mutant inhibits binding to the LDS of LC3C. I, HEK293 cells were transiently transfected with FLAG-tagged constructs of STK3 WT and LIR mutant (MVI/AAA), and whole-cell lysates were incubated with recombinant GST or GST–ATG8s family proteins. 
GST-pulldown assays using extracts from HeLa cells expressing the FLAG–STK3 or the FLAG–STK3 MVI/AAA CLIR mutant verified the strong binding of FLAG–STK3 to GABARAP and LC3C, whereas the CLIR mutant FLAG–STK3 MVI/AAA did not show significant binding.
Furthermore, the GABARAP Y49A LDS mutant displayed strongly-reduced binding to FLAG–STK3 (Fig. 1I).
The annotation include the non canonical CLIR motif MVI at position 365 – 367.
Protein: DP01461 (UniProt Q13188)
Region: residues 365	to 367
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
TK3 interacts with LC3C and GABARAP via a CLIR
Figure 1. STK3 interacts with LC3C and GABARAP via a C-type atypical LIR motif. G, and H, GST pulldown analyses of binding of Myc-tagged STK3 WT and LIR mutant translated in vitro in the presence of [35S]methionine to GST-LC3C (G) or Myc-tagged STK3 WT translated in vitro in the presence of [35S]methionine to GST-LC3C or GST-LC3C F58A (H). The F58A mutant inhibits binding to the LDS of LC3C. I, HEK293 cells were transiently transfected with FLAG-tagged constructs of STK3 WT and LIR mutant (MVI/AAA), and whole-cell lysates were incubated with recombinant GST or GST–ATG8s family proteins. 
GST-pulldown assays using extracts from HeLa cells expressing the FLAG–STK3 or the FLAG–STK3 MVI/AAA CLIR mutant verified the strong binding of FLAG–STK3 to GABARAP and LC3C, whereas the CLIR mutant FLAG–STK3 MVI/AAA did not show significant binding.
Furthermore, the GABARAP Y49A LDS mutant displayed strongly-reduced binding to FLAG–STK3 (Fig. 1I).
The annotation include the non canonical CLIR motif MVI at position 365 – 367.
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 22	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density in the PDB indicates this region is disordered.
Cross-references: PDB:4IMY
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 2	to 73
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Tandem  alanine  replacements  in  residues  3–32,  which  flank  the ordered  CycT1  contacts  in  the  crystal  structure,  showed  significant  but generally  smaller effects  on AFF4 transcriptional stimulation activity. These results implicate the P-TEFb binding site, as well as the flanking flexible sequences, in the function of the AFF4 N-terminal segment.
Residues 2–73 of AFF4, for example, are sufficient to bind P-TEFb through the CycT1 subunit, and a peptide encompassing AFF42–73 folds upon binding CycT1.
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 1	to 300
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
AFF41–300, AFF4300–600, and AFF4600–900 were hypersensitive to proteinase K (Fig. 2B). Limited proteolysis failed to produce large, stable fragments of these AFF4 polypeptides, suggesting intrinsic disorder over the entire sequence.
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 300	to 600
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
AFF41–300, AFF4300–600, and AFF4600–900 were hypersensitive to proteinase K (Fig. 2B). Limited proteolysis failed to produce large, stable fragments of these AFF4 polypeptides, suggesting intrinsic disorder over the entire sequence.
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 600	to 900
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
AFF41–300, AFF4300–600, and AFF4600–900 were hypersensitive to proteinase K (Fig. 2B). Limited proteolysis failed to produce large, stable fragments of these AFF4 polypeptides, suggesting intrinsic disorder over the entire sequence.
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 5	to 23
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 2–73 of AFF4, for example, are sufficient to bind P-TEFb through the CycT1 subunit, and a peptide encompassing AFF42–73 folds upon binding CycT1. 
Cross-references: PDB:4IMY
Protein: DP01463 (UniProt Q9UHB7)
Region: residues 36	to 69
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 2–73 of AFF4, for example, are sufficient to bind P-TEFb through the CycT1 subunit, and a peptide encompassing AFF42–73 folds upon binding CycT1. 
Cross-references: PDB:4IMY
Protein: DP01464 (UniProt P28229)
Region: residues 265	to 332
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In general, the structure of the Cx45, Cx43, and Cx40 CT domains are predominantly intrinsically disordered with varying degrees of a-helical content... The Cx45CT domain contains the largest amount of a-helical structure (19% total a-helical content), which is within one region (A333-N361).
Protein: DP01464 (UniProt P28229)
Region: residues 265	to 332
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The data are characteristic of a protein that contains both a-helical and random coil structures... The CD data indicate that Cx45CT residues A333-N361 are predominantly a-helical.
Protein: DP01464 (UniProt P28229)
Region: residues 265	to 332
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
all of the molecular partners studied here interacted in the intrinsically disordered regions of the Cx45CT
Protein: DP01464 (UniProt P28229)
Region: residues 362	to 396
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In general, the structure of the Cx45, Cx43, and Cx40 CT domains are predominantly intrinsically disordered with varying degrees of a-helical content... The Cx45CT domain contains the largest amount of a-helical structure (19% total a-helical content), which is within one region (A333-N361).
Protein: DP01464 (UniProt P28229)
Region: residues 362	to 396
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The data are characteristic of a protein that contains both a-helical and random coil structures... The CD data indicate that Cx45CT residues A333-N361 are predominantly a-helical.
Protein: DP01465 (UniProt Q8IW19)
Region: residues 399	to 420
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
ZF1 and ZF2 are well-struc- tured, nearly identical in their folds (rmsd 1⁄4 1.1 Å), and are con- nected via a 22-residue linker (residues 399–420), which appears to be largely flexible thus causing some degree of freedom in the domain orientation
Protein: DP01465 (UniProt Q8IW19)
Region: residues 399	to 420
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Collectively, our structure and NMR data show that APLF TZF is made up with two relatively independent domains connected by a largely flexible linker due to the high degree of internal mobility of residues G406–D416.
Protein: DP01465 (UniProt Q8IW19)
Region: residues 450	to 511
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All backbone amide protons resonate in a narrow
spectral region between 7.8 and 8.7 ppm, indicating
that APLFAD is mostly unstructured in solution.
Protein: DP01465 (UniProt Q8IW19)
Region: residues 450	to 511
Annotation: protein folding chaperone (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We have performed structural investigation
on the recognition of H2A-H2B dimers and we present evidence that APLF can function as a true H2AH2B
chaperone.
Protein: DP01465 (UniProt Q8IW19)
Region: residues 450	to 511
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We find that APLFAD binds comparably to both (H3-
H4)2 and H2A-H2B, implying that APLF is a generic histone
chaperone without specificity for either type of histone
complex.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1658	to 1856
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
It exhibits a reduced chemical shift dispersion, especially in the 1H dimension between 8.5 and 7.5 ppm (Fig. 1C), which is a characteristic of the intrinsically disordered proteins (42).
We carried out detailed characterization of a 199-aa-long CHIKV HVD by NMR spectroscopy at atomic resolution. The results revealed the absence of stable secondary structures in this domain and clearly demonstrated that CHIKV HVD was present in solution in a disordered conformation.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1658	to 1856
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
 In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1658	to 1856
Annotation: molecular adaptor activity (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
 In vertebrate cells, CHIKV HVD also coimmunoprecipitated cellular SH3-binding proteins BIN1, CD2AP, and SH3KBP1. In mosquito C7/10 cells, it interacted with A0A182G3T6, the mosquito BIN1 homolog (Fig. 6B). Interestingly, isolation of CD2AP/SH3KBP1 and BIN1 was strongly dependent on the cell type. In human Huh7 and mouse NIH 3T3 cells (35), BIN1, but not CD2AP or SH3KBP1, efficiently interacted with CHIKV HVD. However, in another human cell line, HEK 293 cells, CHIKV HVD preferentially interacted with CD2AP and SH3KBP1, but not with BIN1.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1658	to 1856
Annotation: viral life cycle (Biological process)
Evidence: green fluorescent protein reporter gene assay evidence used in manual assertion
Supporting statements:
In the case of CHIKV, G3BP binding is particularly critical. In contrast to the results of the studies performed on SINV and SFV, deletion of even a single element of the G3BP-binding HVD repeat had a strong negative effect on CHIKV replication in both vertebrate and mosquito cells (Fig. 2) (34). Deletion of both elements, in turn, completely abrogated virus replication.
These experimental data strongly suggested that HVDs play critical roles in the adaptation of CHIKV and EILV to replication in particular cell types. Despite having very similar G3BP-binding repeating peptides, heterologous HVDs changed cell specificities of replication for both viruses. This was a strong support for the hypothesis that HVD fragments located upstream of the carboxy-terminal G3BP/Rin-binding repeat play an indispensable role in CHIKV replication.
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1761	to 1856
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Western blot analysis with NAP1L1-specific Abs also definitively detected the latter protein in the co-IP samples generated on the cells infected with VEErep/Flag-GFP-ABCD but not with any other constructs, including VEErep/Flag-GFP-ABC and VEErep/Flag-GFP-123D (Fig. 8B). The most plausible explanation for the lack of NAP1L1 binding to CHIKV HVD deletion mutant constructs was that NAP1L1 binding requires the presence of intact aa sequences of both fragments C and D. Indeed, two isoforms of NAP1L1 were readily detectable in the samples generated from the cells infected with replicons expressing Flag-GFP-12CD and Flag-GFP-12(C3)D fusions (Fig. 8C). This was an indication that NAP1L1 interacts with HVD on the border between C and D fragments (see Fig. 11).
IDR in the publication is 100% identical to this Uniprot sequence.
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1658	to 1856
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The assignment data unambiguously proved that CHIKV HVD is disordered in solution (Supplementary Fig. 2) and allowed us to characterize in detail its interactions with the SH3-binding domains of CD2AP protein.
Cross-references: BMRB:27868
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1758	to 1775
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The most significant changes in the chemical shift (2 standard deviations, 2σ) were found in three sites: aa 70–83 (Site 1), aa 101–111 (Site 2) and aa 164–172 (Site 3).
As was found for Site 1, the resonances of the residues in the docking site (aa 101–105) for SH3-A and SH3-B complexes were broadening with increasing concentration of the SH3 domains. The signals also became undetectable at saturation point (Supplementary Fig. 9). For the SH3-C complex, the corresponding 1H–15N correlation peaks moved linearly towards the chemical shifts of the bound state.
However, in the experiments with SH3-All, the Site 2-specific signals of residues 101 to 105 were already not detected at the first point of titration, at ratio 0.1:1 (Fig. 4 and Supplementary Fig. 9). This was an indication of a stronger affinity of SH3-All, compared to those of the individual domains. For aa 108R-111L, the CSP trajectories and their maximums were identical to the CSP signatures observed for binding of the SH3-A domain to CHIKV HVD (Fig. 4 and Supplementary Fig. 10).
Protein: DP01466 (UniProt A4L7I2)
Region: residues 1727	to 1741
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The most significant changes in the chemical shift (2 standard deviations, 2σ) were found in three sites: aa 70–83 (Site 1), aa 101–111 (Site 2) and aa 164–172 (Site 3).
As was found for Site 1, the resonances of the residues in the docking site (aa 101–105) for SH3-A and SH3-B complexes were broadening with increasing concentration of the SH3 domains. The signals also became undetectable at saturation point (Supplementary Fig. 9). For the SH3-C complex, the corresponding 1H–15N correlation peaks moved linearly towards the chemical shifts of the bound state.
However, in the experiments with SH3-All, the Site 2-specific signals of residues 101 to 105 were already not detected at the first point of titration, at ratio 0.1:1 (Fig. 4 and Supplementary Fig. 9). This was an indication of a stronger affinity of SH3-All, compared to those of the individual domains. For aa 108R-111L, the CSP trajectories and their maximums were identical to the CSP signatures observed for binding of the SH3-A domain to CHIKV HVD (Fig. 4 and Supplementary Fig. 10).
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Quite unexpectedly, the CD spectrum of DCL1-A indicates that the polypeptide is disordered (Figure 2C) that the polypeptide is disordered
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We expressed the protein construct labeled with 15N, and we found that the 1H-15N-HMQC spectrum of DCL1-A shows a very limited dispersion, confirming that this domain does not fold by itself (Figure 2A).
Despite showing a poorly dispersed 1H-15N-HMQC spectrum DCL1-A appears to have some residual structure, since titrating the protein with Urea results in substantial chemical shift changes for most of the signals. The final state (8M Urea) shows a much better defined spectrum (Supplementary Figure S3), characteristic of fully unfolded proteins, with narrow lines due to fast conformational averaging. This suggests that the free protein is not completely unstructured.
Cross-references: BMRB:19105
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
dsDNA binding induces minor changes in the secondary structure of DCL1-A (green vs. blue spectra), but the change in conformational sampling is negligible compared to that seen in the dsRNA complex (pink).
Protein: DP01467 (UniProt Q9SP32)
Region: residues 1732	to 1811
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The 1H15N-TROSY spectrum of the complex displays a new set of well-dispersed signals, showing that the protein acquires a more ordered fold in the bound form  ​(Figure 4A). The new set of signals coexists with the signals corresponding to the unfolded protein, showing that the free and bound forms of the protein are in slow exchange in the NMR timescale. In order to confirm that both protein species are functional and in conformational exchange between each other we acquired ZZ exchange spectra on the sample and found the corresponding exchange crosspeaks, indicating that the folded and unfolded form are in equilibrium (Figure ​4B and Supplementary Figure S8).
These experiments indicate that DCL1-A folding is specifically induced by dsRNA.
Cross-references: BMRB:19104