LiteFold/DisProt huggingface dataset:
Protein: DP04167 (UniProt Q8N6T7)
Region: residues 272	to 355
Annotation: protein import into nucleus (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
Finally, we analyzed the cellular localization of the isolated CTE and NTE sequences of SIRT6 fused to GFP. The CTE (and Δcore) were sufficient to direct nuclear localization of GFP, generating a pattern indistinguishable from that of full-length SIRT6 fused to GFP (Figure 2C). In contrast, the localization pattern of the NTE was indistinguishable from that of GFP alone (Figure 2C).
The CTE construct comprises the region 272-355.
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues from PDB structure 2FIC.
Cross-references: PDB:2FIC
Protein: DP04169 (UniProt O00499)
Region: residues 12	to 30
Annotation: lipid binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The micelle environment generally stabilizes the helix, leading to a range of α-helicities of 40 to 50% (SDS1: 48%; SDS3: 50%; DPC: 40%) for residues 12–30 during the final simulated 20 ns.
Cross-references: PDB:2RND
PDB:2RMY
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-BAR peptide is unstructured in aqueous solution (Fig. 1 b, solid black line).
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-BAR peptide is unstructured in aqueous solution (Fig. 1 b, solid black line). As in the full-length protein, the ellipticity minima at 208 and 222 nm indicate that the peptide takes on a helical structure when bound to liposomes or micelles. The CD spectra of the N-BAR peptide in brain lipid liposomes or DPC or SDS micelles are virtually identical, indicating a similar secondary structure under these conditions (Fig. 1 b).
In the presence of liposomes (dashed dark gray line), SDS (solid gray line) or DPC (black dashed line) micelles, the peptide becomes structured.
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The isolated N-BAR peptide is unstructured in aqueous solution (Fig. 1 b, solid black line). As in the full-length protein, the ellipticity minima at 208 and 222 nm indicate that the peptide takes on a helical structure when bound to liposomes or micelles. The CD spectra of the N-BAR peptide in brain lipid liposomes or DPC or SDS micelles are virtually identical, indicating a similar secondary structure under these conditions (Fig. 1 b).
In the presence of liposomes (dashed dark gray line), SDS (solid gray line) or DPC (black dashed line) micelles, the peptide becomes structured.
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Binding of the N-BAR peptide to micelles results in a deviation of the backbone and, more obviously, the side-chain resonances in the 15N-HSQC spectrum (Fig. 2 b) from the random coil chemical shifts dominating the spectrum in aqueous solution (Fig. 2 a).
Protein: DP04169 (UniProt O00499)
Region: residues 8	to 33
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Binding of the N-BAR peptide to micelles results in a deviation of the backbone and, more obviously, the side-chain resonances in the 15N-HSQC spectrum (Fig. 2 b) from the random coil chemical shifts dominating the spectrum in aqueous solution (Fig. 2 a). This finding confirms the interaction of N-BAR with the micellar environment and the induction of a defined secondary structure in SDS or DPC observed by far-UV CD spectra.
Residues 8–34 in SDS and 10–34 in DPC micelles are well-ordered with a heavy atom root mean-square deviation < 1.1 Å.
Protein: DP04169 (UniProt O00499)
Region: residues 10	to 33
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Binding of the N-BAR peptide to micelles results in a deviation of the backbone and, more obviously, the side-chain resonances in the 15N-HSQC spectrum (Fig. 2 b) from the random coil chemical shifts dominating the spectrum in aqueous solution (Fig. 2 a). This finding confirms the interaction of N-BAR with the micellar environment and the induction of a defined secondary structure in SDS or DPC observed by far-UV CD spectra.
 Residues 8–34 in SDS and 10–34 in DPC micelles are well-ordered with a heavy atom root mean-square deviation < 1.1 Å.
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: lipid tube assembly (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The human amphiphysin N-BAR domain can constrict liposomes into tubules but leads to vesiculation at higher protein concentrations (Fig. 8 b) (13). A deletion mutant lacking the N-terminal amphipathic helix (BAR) had much less influence on the liposome morphology (Fig. 8 c). In addition to extensive vesiculation, tube formation was observed for the N-BAR peptide (Fig. 8, d and e) and the extended 1–44 residue N-BAR peptide (Fig. 8 f).
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: membrane fusion (Biological process)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
FRET-based membrane fusion assays yield a more quantitative measure of the membrane fusion properties of the different BAR domain constructs. Liposomes were prepared with fluorescence-labeled lipids and subsequently mixed with unlabeled liposomes; fusion of labeled with unlabeled liposomes can be followed by the quench of the FRET signal concomitant with an increase of the donor fluorescence at 530 nm. Fig. 8, g and h, shows membrane fusion for the N-BAR domain and the N-BAR peptides but not for the BAR domain lacking helix-0.
Protein: DP04169 (UniProt O00499)
Region: residues 1	to 33
Annotation: membrane tubulation (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The human amphiphysin N-BAR domain can constrict liposomes into tubules but leads to vesiculation at higher protein concentrations (Fig. 8 b) (13). A deletion mutant lacking the N-terminal amphipathic helix (BAR) had much less influence on the liposome morphology (Fig. 8 c). In addition to extensive vesiculation, tube formation was observed for the N-BAR peptide (Fig. 8, d and e) and the extended 1–44 residue N-BAR peptide (Fig. 8 f).
FRET-based membrane fusion assays yield a more quantitative measure of the membrane fusion properties of the different BAR domain constructs. Liposomes were prepared with fluorescence-labeled lipids and subsequently mixed with unlabeled liposomes; fusion of labeled with unlabeled liposomes can be followed by the quench of the FRET signal concomitant with an increase of the donor fluorescence at 530 nm. Fig. 8, g and h, shows membrane fusion for the N-BAR domain and the N-BAR peptides but not for the BAR domain lacking helix-0.
Protein: DP04170 (UniProt P34174)
Region: residues 151	to 164
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To further characterize the apparent increased structural disorder in the C-terminal tail and the loop L2, we measured 15 N{1H}-NOEs (data not shown). These show clearly that the tail of residues 129-142 is flexibly disordered, and that the loop L2 of residues 33-45 also shows increased mobility. For both of these polypeptide segments, medium-range 1H-1H NOEs are scarce and there are no long-range NOEs, which is compatible with a fl£exibly disordered conformation.
The disordered C-terminal tail described in the publication, 129-142, corresponds to region 151-164 of Bombyx mori PBP due to the presence of a signal peptide.
Cross-references: PDB:1LS8
Protein: DP04171 (UniProt Q92784-1)
Region: residues 60	to 200
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
Predictions, spectroscopy, and dynamic light scattering have revealed a high content in disorder: prevalence of random coil, aromatic residues partially to fully exposed to the solvent, and large hydrodynamic diameters.
From the N-terminus, the disorder profile includes the 2/3 domain (and beyond), which is considered mostly ordered (residues 1 to 90), although disorder scores varying between 0.2 and 0.5 indicate some chain flexibility, especially from residues 60 to 90. This is followed by a 110-residue-long IDR (IDR-1) up to the C2H2 zinc finger (ZnF), where the disorder score drops below the 0.5 threshold (residues 199 to 220), though retaining some flexibility.
Predictions and experimental evidence have been consistent with both isoforms being highly disordered proteins. CD spectroscopy has revealed similar footprints dominated by random coil, and measured hydrodynamic diameters by DLS indicate that they adopt expanded conformations.
The boundaries of this disordered region were determined by the combination of the structural predictors used in the publication (PONDR and IUPred), AlphaFold and Mobi DB.
Protein: DP04171 (UniProt Q92784-1)
Region: residues 222	to 259
Annotation: disorder (Structural state)
Evidence: combinatorial experimental and curator inference evidence used in manual assertion
Supporting statements:
Predictions, spectroscopy, and dynamic light scattering have revealed a high content in disorder: prevalence of random coil, aromatic residues partially to fully exposed to the solvent, and large hydrodynamic diameters.
A second shorter 40-residue-long IDR (IDR-2) is found between the C2H2 and PHD1 ZnFs (residues 221–260), followed by a gain in order at the level of the PHD1 finger (residues 261–292).
Predictions and experimental evidence have been consistent with both isoforms being highly disordered proteins. CD spectroscopy has revealed similar footprints dominated by random coil, and measured hydrodynamic diameters by DLS indicate that they adopt expanded conformations.
The boundaries of this disordered region were determined by the combination of the structural predictors used in the publication (PONDR and IUPred), AlphaFold and Mobi DB.
Protein: DP04172 (UniProt Q61474)
Region: residues 185	to 200
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal region, Gln185–Ser200, was unstructured in the free form.
Cross-references: PDB:5X3Y
Protein: DP04172 (UniProt Q61474)
Region: residues 194	to 362
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The chemical shift assignments for the IDRs of Musashi-1 (residues 194–362; BMRB access number: 50204) are shown in Figure 2A (pH 5.5, 283 K).
 Although the PASTA algorithm [40] predicts four α-helices based on the primary sequence (Figure 2B), secondary chemical shift analysis indicates that just two regions, residues ~208–218 and ~270–284, form transient α-helices (Figure 2C–E), with populations (predicted using the δ2D algorithm [41] derived from the molecular dynamics simulation and experimental observations of conformational equilibrium of multiple states, using Cα, Cβ, C’, HN, and NH chemical shifts) of 28% and 45% at most (Figure 2F).
Cross-references: BMRB:50204
Protein: DP04172 (UniProt Q61474)
Region: residues 194	to 362
Annotation: protein homodimerization activity (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
Micrographs of the oligomers that form at 293 and 303 K are shown in Figure 3D.
Protein: DP04172 (UniProt Q61474)
Region: residues 194	to 362
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The protein is prone to aggregation and proline-rich (~12% in the sequence), so a specific assignment strategy was used, as described in the Material and Methods section and the Supplementary Information.
The precipitation of the protein made it difficult to use CD spectroscopy to estimate its secondary structure, as the Δε values (Equation (1)) used as input for the program became more uncertain as aggregates formed and the signal intensity decreased.
Protein: DP04173 (UniProt Q9BUR4)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7BGB
EMDB:12177
Protein: DP04173 (UniProt Q9BUR4)
Region: residues 199	to 209
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7BGB
EMDB:12177
Protein: DP04173 (UniProt Q9BUR4)
Region: residues 442	to 452
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7BGB
EMDB:12177
Protein: DP04173 (UniProt Q9BUR4)
Region: residues 486	to 503
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7BGB
EMDB:12177
Protein: DP04173 (UniProt Q9BUR4)
Region: residues 511	to 548
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7BGB
EMDB:12177
Protein: DP04174 (UniProt Q12211)
Region: residues 1	to 71
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04174 (UniProt Q12211)
Region: residues 254	to 266
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04174 (UniProt Q12211)
Region: residues 254	to 266
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04174 (UniProt Q12211)
Region: residues 464	to 483
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04174 (UniProt Q12211)
Region: residues 464	to 483
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04174 (UniProt Q12211)
Region: residues 494	to 544
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density maps from molecular replacement and subsequent rounds of refinement displayed well-ordered density for most of the protein chain (the first 70 residues, last 49 residues, and four subsequent surface loops ranging in length from 2 to 19 residues were disordered) and the first 12 bases of the RNA substrate (the final 6 base pairs were also disordered).
Cross-references: PDB:7R9F
Protein: DP04175 (UniProt Q08647)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While it is not mentioned in the publication, this region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: PDB:7MZV
Protein: DP04175 (UniProt Q08647)
Region: residues 485	to 506
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While it is not mentioned in the publication, this region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: PDB:7MZV
Protein: DP04175 (UniProt Q08647)
Region: residues 662	to 676
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While it is not mentioned in the publication, this region lacks electron density in the PDB structure, indicating it is disordered.
Cross-references: PDB:7MZV
Protein: DP04175 (UniProt Q08647)
Region: residues 87	to 201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
However, we were unable to obtain a structure solution for insertion domain one, which necessitated the growth of Se-Met Pus7 crystals.
The electron density corresponding to the insertion domain is overall poor and of rather low resolution, as also reflected in the very high average B-factors (165.02) as compared to the average B-factors (117.44) for the rest of the protein (Figure S2E).
The B-factor values exceeding 170 in this region suggest a high degree of flexibility.
Cross-references: PDB:7MZV
Protein: DP04176 (UniProt P9WHP7)
Region: residues 112	to 139
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 115-142 in MTB-TRUB-A and residues 112-139 in MTB-TRUB-B are missing in the electron density map (henceforth referred to as the disordered region) and are not modeled.
Cross-references: PDB:1SGV
Protein: DP04177 (UniProt P05114)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The desired molecular weight of 10.6 kDa was confirmed by mass spectrometry, however HMGN1 runs abnormally on SDS-PAGE, showing an apparent molecular weight of ∼22 kDa (Fig. 2b and d), likely due to its high content of charged residues and disordered nature.
Protein: DP04177 (UniProt P05114)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The lack of characteristic alpha-helix or beta-sheet maxima and minima in the CD spectrum (Fig. 2c) also gives evidence for the absence of secondary structural features.
Protein: DP04177 (UniProt P05114)
Region: residues 1	to 100
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Three-dimensional HNCO, HNCA, HN(CA)CB, HN(CO)CA, HN(CO)(CA)CB, HN(CA)CO, HN(CO)(CA)(N)NH, and HN(CA)(N)NH spectra were acquired on a 700 MHz NMR spectrometer equipped with a cryoprobe and showed sharp signals typical of intrinsically disordered proteins.
Protein: DP04177 (UniProt P05114)
Region: residues 11	to 64
Annotation: nucleosome binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Overall, the results show that all HMGN1 variants bind to nucleosomes and the major band at 2 : 1 HMGN1 : nucleosome ratios corresponds to two HMGN1 molecules per nucleosome (Fig. 5a), as would be expected from binding of one HMGN1 to each face of the nucleosome.
Truncated HMGN1 variants in which the N-terminal residues (1–10) or C-terminal residues (65–99) were missing were also compared with full-length HMGN1 for their nucleosome-binding properties, as shown in ESI,† Fig. S9.1. Considering the lower molecular weights, the truncated variants show similar nucleosome binding to full-length HMGN1, showing that the N- and C-terminal regions are not directly involved in nucleosome core binding.
Protein: DP04177 (UniProt P05114)
Region: residues 11	to 64
Annotation: nucleosomal DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Experiments in which the HMGN1 variants were mixed with DNA (147 bp AlexaFluor488 labelled DNA containing the 601 nucleosome positioning sequence, Supplementary Data Fig. S9.2, ESI†) indicated that there is no difference in binding of the HNGN1 variants to naked DNA.
Protein: DP04178 (UniProt O14746)
Region: residues 180	to 321
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:7QXS
PDB:7QXB
PDB:7QXA
EMDB:14197
EMDB:14196