LiteFold/DisProt huggingface dataset:
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 31
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Consistent with these observations, the CaM·MA-(8–43) structure shows that residues Asp14–Arg20 and Leu31–Glu40 of MA-(8–43) are α-helical, whereas residues Leu21–Gln28 connecting the two MA α-helices, residues Leu8–Leu13 and Leu41–Arg43, lack a regular secondary structure (Fig. 5A).
Region comprised between 14-20 residues is too short to be considered structured. Despite this publication is about Human immunodeficiency virus type 1 group M subtype B (isolate NY5) matrix protein, IDR is 100% identical.
Cross-references: PDB:2MGU
BMRB:19604
Protein: DP00410 (UniProt P12497)
Region: residues 44	to 114
Annotation: order to disorder (Structural transition)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Digestion reactions were conducted on the myr(−)MA-CaM complex as well as unbound myr(−)MA and CaM. The complex was subjected to limited proteolysis by the addition of thermolysin (from B. thermoproteolyticus rokko) at 1:1000 (enzyme:complex) molar ratio (see “Experimental Procedures” for more details). After 2 h, the MA protein was readily cleaved, whereas the CaM protein was intact (Fig. 6). Digestion of the complex has resulted in an ∼5-kDa MA peptide that was resistant to proteolysis. Analysis of the digestion products by mass spectrometry revealed that the abundant MA species that was resistant to proteolysis is a peptide spanning residues 7–43 with monoisotopic mass of 4403.47 Da (Fig. 6) as identified by both exact mass measurements and tandem mass spectrometric sequencing. Another closely related minor species for residues 7–44 was also detected (supplemental Fig. S3). On the other hand, digestion of unbound MA resulted in a cleavage of a flexible helix on the C-terminal domain leaving intact residues 1–114 (Fig. 6).
In addition, it appears that when compared with the unbound MA protein, CaM binding to MA induced significant conformational changes that facilitated cleavage by thermolysin.
Protein: DP00410 (UniProt P12497)
Region: residues 44	to 132
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
Digestion of the complex has resulted in an ∼5-kDa MA peptide that was resistant to proteolysis. Analysis of the digestion products by mass spectrometry revealed that the abundant MA species that was resistant to proteolysis is a peptide spanning residues 7–43 with monoisotopic mass of 4403.47 Da (Fig. 6) as identified by both exact mass measurements and tandem mass spectrometric sequencing.
Protein: DP00410 (UniProt P12497)
Region: residues 115	to 132
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
On the other hand, digestion of unbound MA resulted in a cleavage of a flexible helix on the C-terminal domain leaving intact residues 1–114 (Fig. 6).
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the free peptide displays a negative band at ∼200 nm, consistent with a random coil, whereas that of the CaM protein shows two minima at 208 and 222 nm, consistent with a helical structure of the protein.
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the free peptide displays a negative band at ∼200 nm, consistent with a random coil, whereas that of the CaM protein shows two minima at 208 and 222 nm, consistent with a helical structure of the protein. The CD spectrum of the complex is similar to that of the CaM protein, with features distinctive of α-helical type (supplemental Fig. S5). Binding of MA-(8–43) results only in a slight increase of CD minima of CaM, suggesting an increase in the α-helical character.
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The two-dimensional HSQC data obtained for a 15N-labeled MA-(8–43) shows a narrow dispersion of the amide proton resonances, indicating a lack of ordered structure (supplemental Fig. S6).
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The two-dimensional HSQC data obtained for a 15N-labeled MA-(8–43) shows a narrow dispersion of the amide proton resonances, indicating a lack of ordered structure (supplemental Fig. S6). Upon binding of CaM, almost all 1H,15N signals of MA-(8–43) exhibited substantial chemical shift changes resulting in large chemical shift dispersion, which indicates that the peptide adopts an ordered structure upon binding to CaM.
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Digestion of the complex has resulted in an ∼5-kDa MA peptide that was resistant to proteolysis. Analysis of the digestion products by mass spectrometry revealed that the abundant MA species that was resistant to proteolysis is a peptide spanning residues 7–43 with monoisotopic mass of 4403.47 Da (Fig. 6) as identified by both exact mass measurements and tandem mass spectrometric sequencing.

Proteolysis data clearly indicate that MA residues 7–43 are protected upon binding to CaM.
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding of CaM, almost all 1H,15N signals of MA-(8–43) exhibited substantial chemical shift changes resulting in large chemical shift dispersion, which indicates that the peptide adopts an ordered structure upon binding to CaM.
Protein: DP00410 (UniProt P12497)
Region: residues 8	to 43
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
 Thermodynamic data revealed that MA-(8–43) binds to CaM with 1:1 stoichiometry (Fig. 7). Strikingly, the binding affinity is much tighter (Kd = 25 nm) than that observed for all peptides described above (Table 1). What is even more intriguing is that the binding affinity of MA-(8–43) to CaM is 32-fold tighter than that of MA-(11–46), suggesting that residues Leu-8, Ser-9, and Gly-10 of MA contribute to the stabilization of the complex.
To assess the role of electrostatic and hydrophobic factors, ITC data were obtained for MA-(8–43) as titrated with CaM at high salt concentration (500 mm NaCl). Our data revealed that the binding affinity (Kd = 60 nm) is only reduced by ∼2-fold upon increasing the salt concentration from 50 to 500 mm (Fig. 7), indicating that electrostatic interactions are not important in stabilizing the CaM-MA-(8–43) complex. This result is also consistent with that obtained for CaM binding to the full-length MA protein (46), indicating that interactions between CaM and MA-(8–43) are mainly hydrophobic.
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra of the Rev ARM peptide in physiological buffer exhibited a minimum around 200 nm, typical of an unfolded state (Fig. 1 A).
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To obtain residue-specific information regarding the Rev ARM peptide, we recorded 1HN,15N-HSQC spectra (Fig. 2). In aqueous solution, the peptide shows little dispersion of the resonances (Fig. 2 B), indicative of an unfolded peptide and in accordance with the CD data.
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 5 B shows that the [1HN],15N hetNOE values for Rev ARM in aqueous solution at pH 7.4 average 0.47 for residues T34–R50, consistent with a disordered peptide. In contrast, the hetNOEs of the Rev ARM peptide in complex with RRE StemIIB average 0.83 for residues T34–R50, and in 50% TFE average 0.77 for residues T34–R50. These higher hetNOE values indicate higher backbone rigidity and are typical of a well-ordered secondary structure.
RRE StemIIB it's the RNA binding Rev ARM.
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 5 B shows that the [1HN],15N hetNOE values for Rev ARM in aqueous solution at pH 7.4 average 0.47 for residues T34–R50, consistent with a disordered peptide. In contrast, the hetNOEs of the Rev ARM peptide in complex with RRE StemIIB average 0.83 for residues T34–R50, and in 50% TFE average 0.77 for residues T34–R50. These higher hetNOE values indicate higher backbone rigidity and are typical of a well-ordered secondary structure.
RRE StemIIB it's the RNA binding Rev ARM.
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We further characterized the differences in IA and IIB binding modes using amide proton chemical shifts from 15N HSQC NMR spectra to monitor changes in the peptide-RNA interfaces. There is little peak dispersion of peptide resonances in the absence of RNA (Figure 5C), indicative of a largely unstructured molecule.
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We further characterized the differences in IA and IIB binding modes using amide proton chemical shifts from 15N HSQC NMR spectra to monitor changes in the peptide-RNA interfaces. There is little peak dispersion of peptide resonances in the absence of RNA (Figure 5C), indicative of a largely unstructured molecule. However, we observe substantial amide peak dispersion in the presence of either IIB (red) or IA (blue) RNAs (Figure 5C), including the Hε protons of arginine side chains (Figure 5C inset). The overall upfield shifts observed in both 1H and 15N dimensions is consistent with stabilization of peptide α-helical structure upon binding (Wang and Jardetzky, 2002).
Protein: DP00424 (UniProt P04325)
Region: residues 34	to 50
Annotation: RNA binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Given, the purine-rich internal loop of IA, we asked if this amino acid also is essential for IA binding. Interestingly, mutation of Asn40 had no effect on IA binding. Conversely, mutation of Arg41, which does not affect IIB binding (Tan et al., 1993), showed a reproducible 2-fold decrease in IA affinity (Figure 5A). R38A and R46A mutants showed similar 2-fold reductions in IA affinity but had no effect on IIB, while R43A, R44A, and W45A mutants bound IA like the wild type peptide. Helical wheel projections clearly show that different surfaces of the helix are used to recognize IIB and IA RNAs (Figure 5B).
Protein: DP00424 (UniProt P04325)
Region: residues 35	to 46
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
As shown in a gel mobility shift assay (Figure 2), the addition of Rev normally leads to formation of multimeric complexes with 35S-labelled RRE.
Protein: DP00424 (UniProt P04325)
Region: residues 35	to 46
Annotation: protein binding (Molecular function)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
The experiment demonstrates the specificity of the Rev-importin-β interaction, as importin-β did not bind to the GST-Rev NLS mutant, or to GST protein. This was an unexpected finding, and identifies Rev as the first protein known to contain an NLS specific for the 97 kDa importin-β receptor, and not importin-α.
Protein: DP00424 (UniProt P04325)
Region: residues 35	to 50
Annotation: protein localization to nucleoplasm (Biological process)
Evidence: green fluorescent protein fusion protein localization evidence used in manual assertion
Supporting statements:
Rev–GFP showed typical predominantly nuclear localization (>80% of fluorescence) (Fig. 2A). In contrast, RevM5–GFP fluorescence was apparent mainly in the cytoplasm, with less than 22% of total fluorescence in the nucleus (Fig. 2A).
RevM5 has a mutation in this IDR.
Protein: DP00427 (UniProt P0AFG8)
Region: residues 541	to 557
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our crystallographic studies have shown that two active center loops (an inner loop formed by residues 401–413 and outer loop formed by residues 541–557) of the E1 component of the Escherichia coli pyruvate dehydrogenase complex become organized only on binding a substrate analog that is capable of forming a stable thiamin diphosphate-bound covalent intermediate.
Cross-references: PDB:2QTA
PDB:2QTC
Protein: DP00427 (UniProt P0AFG8)
Region: residues 541	to 557
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
we have demonstrated that disorder to order transformation of active center dynamic loops (particularly the inner loop) modulates steps through LThDP formation. Ordering of loops also facilitates E1ec to E2ec active center communication reconfirming our previous hypothesis, presumably by acting as a recognition site for E2ec lipoyl domain, and acts as a regulatory switch for the next committed step in E1ec catalysis.
Protein: DP00427 (UniProt P0AFG8)
Region: residues 401	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our crystallographic studies have shown that two active center loops (an inner loop formed by residues 401–413 and outer loop formed by residues 541–557) of the E1 component of the Escherichia coli pyruvate dehydrogenase complex become organized only on binding a substrate analog that is capable of forming a stable thiamin diphosphate-bound covalent intermediate.
Cross-references: PDB:2QTA
PDB:2QTC
Protein: DP00427 (UniProt P0AFG8)
Region: residues 401	to 413
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
we have demonstrated that disorder to order transformation of active center dynamic loops (particularly the inner loop) modulates steps through LThDP formation. Ordering of loops also facilitates E1ec to E2ec active center communication reconfirming our previous hypothesis, presumably by acting as a recognition site for E2ec lipoyl domain, and acts as a regulatory switch for the next committed step in E1ec catalysis.
Protein: DP00428 (UniProt P53350)
Region: residues 495	to 506
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Only spanning residues 495-506 are missing from crystal structure 2OGQ, the residues 493, 494 and 507, indicated as boundaries of the disordered loop by the authors are ordered in the structure
After careful comparison of the three models, the main difference arises from the 20-residue loop, which is disordered in the apo and PBD-Cdc25C structures (residues Ala-493–Arg-507 for apo and Glu-488–Arg-507 for the PBD-Cdc25C complex).
Cross-references: PDB:2OGQ
Protein: DP00428 (UniProt P53350)
Region: residues 489	to 506
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Only spanning residues 489-506 are missing from crystal structure 2OJX, the residues 488 and 507, indicated as boundaries of the disordered loop by the authors are ordered in the structure
After careful comparison of the three models, the main difference arises from the 20-residue loop, which is disordered in the apo and PBD-Cdc25C structures (residues Ala-493–Arg-507 for apo and Glu-488–Arg-507 for the PBD-Cdc25C complex).
Cross-references: PDB:2OJX
Protein: DP00428 (UniProt P53350)
Region: residues 489	to 506
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Although the structure of the PBD among the three different crystals is well conserved (SI Fig. 10a), the loop that connects PBI and PBII is ordered only in the case of the PBD-Cdc25C-P complex
Cross-references: PDB:3BZI
Protein: DP00428 (UniProt P53350)
Region: residues 495	to 506
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Although the structure of the PBD among the three different crystals is well conserved (SI Fig. 10a), the loop that connects PBI and PBII is ordered only in the case of the PBD-Cdc25C-P complex
After careful comparison of the three models, the main difference arises from the 20-residue loop, which is disordered in the apo and PBD-Cdc25C structures (residues Ala-493–Arg-507 for apo and Glu-488–Arg-507 for the PBD-Cdc25C complex). This loop [connecting loop (CL)] joins both PB and flanks the binding site of the target peptide (SI Figs. 8 and 10a).
Cross-references: PDB:2OGQ
Protein: DP00428 (UniProt P53350)
Region: residues 489	to 506
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Although the structure of the PBD among the three different crystals is well conserved (SI Fig. 10a), the loop that connects PBI and PBII is ordered only in the case of the PBD-Cdc25C-P complex
After careful comparison of the three models, the main difference arises from the 20-residue loop, which is disordered in the apo and PBD-Cdc25C structures (residues Ala-493–Arg-507 for apo and Glu-488–Arg-507 for the PBD-Cdc25C complex). This loop [connecting loop (CL)] joins both PB and flanks the binding site of the target peptide (SI Figs. 8 and 10a).
Cross-references: PDB:2OJX
Protein: DP00429 (UniProt P32170)
Region: residues 50	to 64
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the refined ``native'' structure (i.e. the SeMet variant), the loop comprising residues 58 through 72 (b1-a1-loop) is completely disordered.
The region the authors are reffering to corresponds to the 50-64 residues of the Uniprot.
Cross-references: PDB:1D8W
Protein: DP00429 (UniProt P32170)
Region: residues 50	to 64
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the refined ``native'' structure (i.e. the SeMet variant), the loop comprising residues 58 through 72 (b1-a1-loop) is completely disordered." Curator statement "The region the authors are reffering to corresponds to the 50-64 residues of the Uniprot.
Cross-references: PDB:1D8W
Protein: DP00429 (UniProt P32170)
Region: residues 50	to 64
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Upon binding of L-rhamnitol, however, this segment, which will be named the b1-a1-loop, closes the top of the (b/a)8-barrel, covers the active site and excludes the bound inhibitor from contact with bulk solvent (Figure 8). The electron density maps and re®nement suggest that the b1-a1-loop becomes essentially as well ordered as neighboring parts of the protein.
It was noted above that the binding of the inhibitor L-rhamnitol, and to a lesser degree the binding of the substrate, L-rhamnose, causes the b1-a1-loop to cover the active site like a lid (Figure 8). 
The structures of complexes of rhamnose isomerase with the inhibitor L-rhamnitol and the natural substrate L-rhamnose were determined and suggest that an extended loop, which is disordered in the native enzyme, becomes ordered on substrate binding, and may exclude bulk solvent during catalysis.
Cross-references: PDB:1DE5
PDB:1DE6
Protein: DP00432 (UniProt P11632)
Region: residues 1	to 25
Annotation: nucleic acid binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Further electrostatic contacts are made by the side-chains of the extended strand and charged region of the amino-terminal tail located in the major groove. In the extended strand region, Lys22 contacts the phosphate of nucleotide T9.
The N-terminal tail residues Arg10, Arg13, Lys14, and Lys16 all make contact with the DNA backbone in most members of the structure ensemble, consistent with their importance in protein–DNA affinity as shown in previous point mutation and deletion studies.
Cross-references: PDB:1J5N
Protein: DP00432 (UniProt P11632)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Helices 1 (residues 27–43) and 2 (residues 47–61) are wrapped around each other to form the short arm of the L. The long arm of the L is formed by helix 3 (residues 64–93) and the extended strand (residues 18–25), which interact extensively via hydrophobic contacts between residues in the extended strand and helix 3, as well as a hydrogen bond between the side-chain carboxyl of Asp77 and the amide proton of Leu25.
This rearrangement of helix 3 probably has only a small energetic cost, as the helix3/extended strand region appears to be inherently flexible for NHP6A as well as other HMGB proteins.
The first nine residues of the N-terminal tail are undefined by the NMR data, and the few assigned resonances have chemical shifts consistent with a random coil.
Cross-references: PDB:1LWM
Protein: DP00435 (UniProt Q01853)
Region: residues 1	to 16
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our crystal structure of murine p97 comprises residues 17–700 and consists of: complete models for the N terminal substrate binding domain and the D1 AAA domain, and a poly-alanine partial model for the D2 AAA domain, in which the α-helical and C-terminal regions are highly disordered (see representative densities in Fig. 1).
Cross-references: PDB:1R7R
Protein: DP00435 (UniProt Q01853)
Region: residues 1	to 16
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our crystal structure of murine p97 comprises residues 17–700 and consists of: complete models for the N terminal substrate binding domain and the D1 AAA domain, and a poly-alanine partial model for the D2 AAA domain, in which the α-helical and C-terminal regions are highly disordered (see representative densities in Fig. 1).