LiteFold/DisProt huggingface dataset:
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Comparison of the spectrum produced by the sum of these two spectra with the spectra obtained experimentally for an equimolar mixture of these two proteins shows there is a significant red shift and increase in the peak magnitude at 184 nm. Changes of this type at this wavelength are primarily associated with a decrease in disordered content. In addition, a small increase of the peak at 222 nm was detected, thus suggesting a concomitant increase in alpha-helix content (Table 1). These results clearly show that the proteins physically interact to form a complex, and upon formation of the complex, they undergo a conformational change consistent with ordering of the MEG-14 partner.
Protein: DP01970 (UniProt M1GUG5)
Region: residues 1	to 86
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Comparison of the spectrum produced by the sum of these two spectra with the spectra obtained experimentally for an equimolar mixture of these two proteins shows there is a significant red shift and increase in the peak magnitude at 184 nm. Changes of this type at this wavelength are primarily associated with a decrease in disordered content. In addition, a small increase of the peak at 222 nm was detected, thus suggesting a concomitant increase in alpha-helix content (Table 1). These results clearly show that the proteins physically interact to form a complex, and upon formation of the complex, they undergo a conformational change consistent with ordering of the MEG-14 partner.
Protein: DP01971 (UniProt P01071)
Region: residues 1	to 181
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
STI presents a CD spectrum of a protein lacking any content in helix, but presenting contributions of β-strands together with a high amount of disordered elements, known as βII class proteins...
Protein: DP01971 (UniProt P01071)
Region: residues 1	to 181
Annotation: disorder (Structural state)
Evidence: synchrotron radiation circular dichroism evidence used in manual assertion
Supporting statements:
Moreover, a small band at ~184 nm could be observed in the SRCD spectra of IDPs, appearing as a shoulder for STI and a small positive peak for MEG-14 (Suppl. Figure 2c). This spectral band can also be attributed to the unordered content of the protein...
Protein: DP01972 (UniProt P13693)
Region: residues 37	to 68
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this work, we combined NMR experiments and MD simulations to characterize the conformational ensemble of the TCTP intrinsically disordered loop, in the presence or not of calcium ions and with or without the phosphorylation of Ser46 and Ser64
Protein: DP01972 (UniProt P13693)
Region: residues 37	to 68
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we propose that the TCTP intrinsically disordered region could play an important role in participating to the interactions with other proteins and non-peptidic ligands, in remodeling the core domain surface, and modulating its accessibility to its partners in response to a variety of cellular conditions, in particularly the presence of calcium ions, or to chemical modifications, such as phosphorylations.
Protein: DP01972 (UniProt P13693)
Region: residues 37	to 68
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
in the loop of residues T39-V66 have 1H–15N NOE values <0.5 with an average value of −0.11 ± 0.49. This clearly indicates that hTCTP has a rather rigid well-folded core and a very flexible loop Lβ5β6, and the rigid to flexible transitions occur in the β-sheet C between these two structural regions. The analysis of R1 and R2 values also indicates the same conclusion.
Protein: DP01972 (UniProt P13693)
Region: residues 42	to 61
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–41 and 62–180, and 1–40 and 64–180 were modeled for chains A and B of the hHRF-1 structure, respectively, and as in the mHRF structure, a substantial portion of the mobile loop region was disordered.
Residues 1–41 and 63–178, and 1–37 and 50–177 were modeled for chains A and B of the hHRF-2 structure, respectively.
Two structures of hHRF are described in the publication, hHRF-1 (PDB:5o9l) and hHRF-2 (PDB:5o9m), the latter revealing a disulphide-linked dimer
Cross-references: PDB:5O9L
Protein: DP01972 (UniProt P13693)
Region: residues 42	to 61
Annotation: molecular function regulator (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
HRF crystal and solution structures have provided little insight into either the formation of disulphide-linked HRF dimers or the ability of HRF to activate mast cells.
The current model for the activity of HRF in mast cell activation involves cross-linking of FcεRI-bound IgE by dimeric HRF, mediated by interactions between HRF and the Fab regions of IgE
Cross-references: PDB:5O9L
Protein: DP01973 (UniProt Q09514)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was detected for residues 1–18, 167–181 and 216–266.
Cross-references: PDB:4BJA
Protein: DP01973 (UniProt Q09514)
Region: residues 167	to 181
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was detected for residues 1–18, 167–181 and 216–266.
Cross-references: PDB:4BJA
Protein: DP01973 (UniProt Q09514)
Region: residues 216	to 266
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was detected for residues 1–18, 167–181 and 216–266.
Cross-references: PDB:4BJA
Protein: DP01974 (UniProt P39748)
Region: residues 45	to 61
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that showed particularly low R2/R1 ratios and low hNOE values were the α2–α3 loop, the arch region and the non-native C-terminal residues. These regions were associated with higher than average B-factors or lacked observable electron density in crystal structures (Figure ​(Figure1D1D–F and Supplementary Figure S2) (11,22).
The lowest S2 values (<0.5) were generally observed in the C-terminal tail, arch and α2–α3 loop residues, thereby indicating that these residues were extremely flexible in solution.
The observable regions of the arch, α2–α3 loop and C-terminal residues showed only small differences (≤1) (Figure ​(Figure4A4A and B), suggesting that these residues were disordered in the free protein.
Cross-references: BMRB:27160
Protein: DP01974 (UniProt P39748)
Region: residues 90	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that showed particularly low R2/R1 ratios and low hNOE values were the α2–α3 loop, the arch region and the non-native C-terminal residues. These regions were associated with higher than average B-factors or lacked observable electron density in crystal structures (Figure ​(Figure1D1D–F and Supplementary Figure S2) (11,22).
The lowest S2 values (<0.5) were generally observed in the C-terminal tail, arch and α2–α3 loop residues, thereby indicating that these residues were extremely flexible in solution.
The observable regions of the arch, α2–α3 loop and C-terminal residues showed only small differences (≤1) (Figure ​(Figure4A4A and B), suggesting that these residues were disordered in the free protein.
Cross-references: BMRB:27160
Protein: DP01974 (UniProt P39748)
Region: residues 330	to 342
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that showed particularly low R2/R1 ratios and low hNOE values were the α2–α3 loop, the arch region and the non-native C-terminal residues. These regions were associated with higher than average B-factors or lacked observable electron density in crystal structures (Figure ​(Figure1D1D–F and Supplementary Figure S2) (11,22).
The lowest S2 values (<0.5) were generally observed in the C-terminal tail, arch and α2–α3 loop residues, thereby indicating that these residues were extremely flexible in solution.
The observable regions of the arch, α2–α3 loop and C-terminal residues showed only small differences (≤1) (Figure ​(Figure4A4A and B), suggesting that these residues were disordered in the free protein.
Cross-references: BMRB:27160
Protein: DP01975 (UniProt O74958)
Region: residues 282	to 327
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, this indicates a highly dynamic domain with a rigid core consisting of the β-sheet and more flexible regions where only broad or no signals were observed. In total, only ∼60% of residues were assignable. This included only 14 confirmed residues in the low-complexity region, suggesting that the remainder of the signals from this region are missing due to line broadening; there were ∼50 fewer cross-peaks than expected, even in the BEST-TROSY experiment with nondeuterated protein.
This N-terminal, low-complexity region does not adopt any formal secondary structure but forms a stably-folded platform encompassing the N-clamp and extending across the YTH domain to contact the C-terminal helix (Fig. 8A).
Cross-references: BMRB:27398
Protein: DP01975 (UniProt O74958)
Region: residues 282	to 327
Annotation: mRNA 3'-UTR binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In contrast, the USR–YTH construct had a binding affinity of 6.1 ± 0.7 nm, ∼25-fold stronger than YTH (Fig. 1D). A similar trend was observed at lower salt (Table 1). Therefore, the USR stabilizes the interaction between the YTH domain and RNA.
The experiment confirmed the bising to an RNA substrate composed of a DSR sequence from the rec8 3′-UTR. DSR stands for determinants of selective removal.
Protein: DP01975 (UniProt O74958)
Region: residues 282	to 327
Annotation: molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Finally, CD spectra recorded for all the constructs showed a similar line shape, although the magnitude of the signal at ∼225 nm increases as more of the low-complexity region is included (Fig. S1B). This can be characteristic of proteins with a molten-globule conformation (29).
Protein: DP01975 (UniProt O74958)
Region: residues 282	to 327
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Surprisingly, 31 additional amide peaks of the low-complexity region could be assigned in the presence of RNA (Fig. 5B, yellow lines). Some of these correspond to residues not observed in the crystal structure. Thus, in the presence of RNA, it is likely that the conformation of the USR and N-clamp become even more constrained, reducing the line broadening in NMR spectra and thereby leading to the appearance of additional protein amide peaks.
On RNA binding, these regions become more ordered and contact or reinforce contacts with RNA.
Cross-references: BMRB:27399
BMRB:27398
Protein: DP01976 (UniProt P35520)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The calculation of the chemical shift index based on the obtained resonance assignment indicates an intrinsically disordered peptide which is supported by the prediction of the web server (IUPRED53) using the primary sequence as sole input.
Cross-references: BMRB:27351
Protein: DP01976 (UniProt P35520)
Region: residues 1	to 40
Annotation: heme binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we report the NMR resonance assignment and heme interaction studies for the N-terminal peptide stretch of CBS. We present NMR-spectral evidence that residues 1–40 constitute an intrinsically disordered region in CBS and interact with heme via a cysteine-proline based motif.
Viewed in totality, the results reported here suggest that the wild-type N-terminal CBS peptide upon heme binding undergoes a conformational change to a hexacoordinated complex with cysteine-15 and histidine-22 as ligands that is sparsely populated and is in exchange with a highly populated free peptide.
We also observed that the single mutation C15S (Fig. 5c) essentially leads to no effect on the relative intensities of the cross peaks in the HSQC spectra upon heme addition. This indicates that mutation of this residue leads to no heme binding and is consistent with the UV/Vis data of this mutant which shows no sharp Soret peak (Supplementary Figure S5) either at ~420 nm (hexacoordination) or at ~370 nm (pentacoordination).
Protein: DP01976 (UniProt P35520)
Region: residues 1	to 40
Annotation: heme binding (Molecular function)
Evidence: spectrophotometry evidence used in manual assertion
Supporting statements:
Thus, this bathochromic effect is characteristic of heme binding and suggests formation of a hexacoordinated state which in CBS involves residues cysteine-15 and histidine-22. The KD value was determined to be 2.18 ± 0.64 μM. According to the best fit possible GB1CBS(1–40) binds to heme with a 1:1 stoichiometry (Fig. 2b).
Protein: DP01977 (UniProt P49736)
Region: residues 1	to 160
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We purified a uniformly 15N labeled sample of human MCM2 (1–160) as a recombinant protein in E. coli and analyzed its structure by standard heteronuclear NMR techniques. Spectral dispersion of NH resonances demonstrates that this fragment is mainly disordered in solution (Supplementary Figure S2 in black).
Protein: DP01977 (UniProt P49736)
Region: residues 69	to 138
Annotation: histone binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon addition of full-length recombinant H3-H4 histones, two subsets of resonances from residues 71–96 and 104–133 vanish and delineate two segments of MCM2 in contact with histones (Figure ​(Figure1C),1C), one of them including the residual helix (107–122) identified above.
The histone binding region could thus be further restricted to the (69–138) segment.
Protein: DP01977 (UniProt P49736)
Region: residues 69	to 138
Annotation: histone binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Affinities of MCM2 (1–160) and MCM2 (69–138) for histones were measured using ITC with dissociation constants of 0.19 ± 0.02 μM (Supplementary Figure S4A, Supplementary Table S1) and 0.24 ± 0.1 μM (Supplementary Figure S4B, Supplementary Table S1), respectively, confirming that the shorter region recapitulates all interactions made by the MCM2 N-terminal region with histones.
Protein: DP01977 (UniProt P49736)
Region: residues 69	to 121
Annotation: histone binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The MCM2 fragment (69–121) wraps around the H3-H4 dimer complex and follows the position of DNA in the nucleosome so that it clearly competes with the binding of DNA.
Cross-references: PDB:4UUZ
Protein: DP01977 (UniProt P49736)
Region: residues 69	to 106
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The MCM2 fragment (69–121) wraps around the H3-H4 dimer complex and follows the position of DNA in the nucleosome so that it clearly competes with the binding of DNA. MCM2 residues G69-L97 and V102-R120 have extensive contacts with both histones H3 and H4 and adopt mainly an extended conformation interrupted by two helical segments: one helical turn involving residues M79-Y81 and a well-defined helix from residues A107 to R118.
Cross-references: PDB:4UUZ
Protein: DP01977 (UniProt P49736)
Region: residues 119	to 138
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The MCM2 fragment (69–121) wraps around the H3-H4 dimer complex and follows the position of DNA in the nucleosome so that it clearly competes with the binding of DNA. MCM2 residues G69-L97 and V102-R120 have extensive contacts with both histones H3 and H4 and adopt mainly an extended conformation interrupted by two helical segments: one helical turn involving residues M79-Y81 and a well-defined helix from residues A107 to R118.
Cross-references: PDB:4UUZ
Protein: DP01977 (UniProt P49736)
Region: residues 107	to 118
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The MCM2 fragment (69–121) wraps around the H3-H4 dimer complex and follows the position of DNA in the nucleosome so that it clearly competes with the binding of DNA. MCM2 residues G69-L97 and V102-R120 have extensive contacts with both histones H3 and H4 and adopt mainly an extended conformation interrupted by two helical segments: one helical turn involving residues M79-Y81 and a well-defined helix from residues A107 to R118.
Cross-references: PDB:4UUZ
Protein: DP01977 (UniProt P49736)
Region: residues 107	to 118
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The MCM2 fragment (69–121) wraps around the H3-H4 dimer complex and follows the position of DNA in the nucleosome so that it clearly competes with the binding of DNA. MCM2 residues G69-L97 and V102-R120 have extensive contacts with both histones H3 and H4 and adopt mainly an extended conformation interrupted by two helical segments: one helical turn involving residues M79-Y81 and a well-defined helix from residues A107 to R118.
Cross-references: PDB:4UUZ
Protein: DP01978 (UniProt Q02554)
Region: residues 351	to 368
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystals contained Cus1(290–368)p but residues 351–368 were disordered.
Protein: DP01979 (UniProt Q6CMF0)
Region: residues 1	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first HEAT repeat (residues 1–39), an intra-
loop of repeat 8 (residues 325–329), repeat 15 (residues 631–656) and repeat 18 (residues 818–828)
are disordered in the final structure.
Cross-references: PDB:5VCH
Protein: DP01979 (UniProt Q6CMF0)
Region: residues 631	to 656
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first HEAT repeat (residues 1–39), an intra-
loop of repeat 8 (residues 325–329), repeat 15 (residues 631–656) and repeat 18 (residues 818–828)
are disordered in the final structure.
Cross-references: PDB:5VCH
Protein: DP01979 (UniProt Q6CMF0)
Region: residues 818	to 828
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first HEAT repeat (residues 1–39), an intra-
loop of repeat 8 (residues 325–329), repeat 15 (residues 631–656) and repeat 18 (residues 818–828)
are disordered in the final structure.
Cross-references: PDB:5VCH
Protein: DP01981 (UniProt P76407)
Region: residues 147	to 158
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered region 147–158...
Cross-references: PDB:2BON
Protein: DP01982 (UniProt Q8HYY9)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 12 residues are disordered and so excluded from the final model.
Cross-references: PDB:1Q8H
Protein: DP01983 (UniProt Q9Q8N4)
Region: residues 151	to 203
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure lacks the 53 C-terminal residues, presumably because these residues were disordered in the crystal packing or degraded during the extended crystallization period.
Cross-references: PDB:5CZ3
Protein: DP01984 (UniProt B4Y891)
Region: residues 1	to 213
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Amino acid residues 1 to 213, which includes the first eleven residues of VP3, were not ordered in the density maps. The lack of ordering of the N-terminus region of VP1–VP3 is consistent with all known parvovirus structures determined to date, except for B19 in which the entire VP2 was observed in a structure determined by cryo-electron microscopy.
Cross-references: PDB:4IOV
Protein: DP01985 (UniProt Q8TEK3)
Region: residues 333	to 416
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Amino acids C-terminal to αK (aa 333–416) are disordered in the structure.
Cross-references: PDB:1NW3
Protein: DP01985 (UniProt Q8TEK3)
Region: residues 333	to 416
Annotation: nucleic acid binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our modeling of hDOT1L-nucleosome interaction suggests that the C-terminal region is near DNA, which led us to hypothesize that the disordered C-terminal positively charged region might be involved in substrate binding by interacting with the negatively charged nucleosomal DNA.
Protein: DP01990 (UniProt P36894)
Region: residues 104	to 120
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In addition, the 45
loop is highly disordered (Figure 2), showing large structural
variations with distances between corresponding CR positions
of up to 10 Å (Phe85)
Cross-references: PDB:2K3G
Protein: DP01990 (UniProt P36894)
Region: residues 104	to 120
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
type I
receptor BMPR-IA, a significant part of the binding interface
with BMP-2 is disordered prior to ligand binding and thus
requires a disorder-to-order transition