LiteFold/DisProt huggingface dataset:
Protein: DP01293 (UniProt Q13542)
Region: residues 1	to 120
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Folding of an intrinsically disordered protein by phosphorylation as a regulatory switch
IDPs such as non-phosphorylated 4E-BP2 have intense peaks with narrow 1HN chemical shift dispersion26.
Protein: DP01293 (UniProt Q13542)
Region: residues 1	to 120
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we show that multisite phosphorylation induces folding of the intrinsically disordered 4E-BP2, the major neural isoform of the family of three mammalian proteins that bind eIF4E and suppress cap-dependent translation initiation.
Cross-references: IntAct:EBI-16080855
Protein: DP01293 (UniProt Q13542)
Region: residues 18	to 62
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We demonstrate that phosphorylation at T37 and T46 induces folding of residues P18–R62 of 4E-BP2 into a four-stranded β-domain that sequesters the helical YXXXXLΦ motif into a partly buried β-strand, blocking its accessibility to eIF4E
Protein: DP01293 (UniProt Q13542)
Region: residues 18	to 62
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We demonstrate that phosphorylation at T37 and T46 induces folding of residues P18–R62 of 4E-BP2 into a four-stranded β-domain that sequesters the helical YXXXXLΦ motif into a partly buried β-strand, blocking its accessibility to eIF4E.
Unlike other IDPs for which phosphorylation only causes downfield chemical shifts of phosphorylated residues27, 4E-BP2 phosphorylation induces widespread downfield and upfield chemical shifts for residues spanning T19–R62, suggesting folding upon phosphorylation (Fig. 1b).
Protein: DP01293 (UniProt Q13542)
Region: residues 18	to 62
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Unlike other IDPs for which phosphorylation only causes downfield chemical shifts of phosphorylated residues27, 4E-BP2 phosphorylation induces widespread downfield and upfield chemical shifts for residues spanning T19–R62, suggesting folding upon phosphorylation (Fig. 1b).
Cross-references: PDB:2MX4
Protein: DP01293 (UniProt Q13542)
Region: residues 1	to 120
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
 In its non-phosphorylated state, 4E-BP2 interacts tightly with eIF4E using both a canonical YXXXXLW motif (starting at Y54) that undergoes a disorder-to-helix transition upon binding and a dyna- mic secondary binding site7–11.
ITC (Extended Data Table 2 and Extended Data Fig. 7) and NMR data were obtained on 4E-BP2 variants to probe the role of electrostatics in folding and reducing eIF4E affinity.
Protein: DP01295 (UniProt Q98XH7)
Region: residues 6	to 14
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
2Fo − Fc and Fo − Fc difference electron density maps showed that Tat-1 and Tat-3 peptides were well lodged in the antigen-binding site of Fab′ (Fig. 2c).
Cross-references: PDB:3O6M
Protein: DP01295 (UniProt Q98XH7)
Region: residues 2	to 16
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
2Fo − Fc and Fo − Fc difference electron density maps showed that Tat-1 and Tat-3 peptides were well lodged in the antigen-binding site of Fab′ (Fig. 2c).
Cross-references: PDB:3O6L
Protein: DP01295 (UniProt Q98XH7)
Region: residues 6	to 14
Annotation: protein binding (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
Thus, mAb 11H6H1 recognizes the full-length active Tat and the smaller 15-mer peptide (Tat-1) and 9-mer minimal epitope (Tat-3) with similar affinities, suggesting that the antibody/peptide interaction is close to that observed with the full-length protein. Moreover, the fact that the 9-mer peptide is recognized with the same affinity as the 15-mer peptide suggests that it indeed contains all the residues necessary for the recognition of Tat by 11H6H1.
Protein: DP01295 (UniProt Q98XH7)
Region: residues 6	to 14
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structures of this 9-mer peptide and of an overlapping 15-mer peptide were determined in complex with Fab′ 11H6H1 at 2.4 Å and 2.1 Å resolution, respectively.
Cross-references: PDB:3O6M
Protein: DP01295 (UniProt Q98XH7)
Region: residues 2	to 16
Annotation: molecular adaptor activity (Molecular function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
The crystal structures of this 9-mer peptide and of an overlapping 15-mer peptide were determined in complex with Fab′ 11H6H1 at 2.4 Å and 2.1 Å resolution, respectively.
Cross-references: PDB:3O6L
Protein: DP01295 (UniProt Q98XH7)
Region: residues 2	to 16
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
Although early NMR structural studies of Tat suggested that Tat was a globular protein devoid of secondary structural elements,19, 20, 21, 22 recent publications have demonstrated that Tat is in fact an intrinsically disordered protein in solution that is able to bind a wide variety of structurally distinct cellular and/or viral biological partners responsible for several biological functions.23, 24 This was further demonstrated by a recent crystallographic study of Tat in complex with the nuclear transcription factor p-TEFb, in which Tat appears elongated, except for short helices around its cysteine-rich domain.
Protein: DP01296 (UniProt Q6BBK3)
Region: residues 1	to 52
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Mass spectroscopy of dissolved crystals confirmed that only the full-length CP12 is contained in the crystals (H.M. and A.K., unpublished observation); therefore, the N-terminal region is largely disordered in the crystal
Protein: DP01296 (UniProt Q6BBK3)
Region: residues 1	to 52
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The GAPDH-CP12 complex structure reveals that the oxidized CP12 becomes partially structured upon GAPDH binding
Cross-references: imex:DIP-59423N
Protein: DP01299 (UniProt Q96273)
Region: residues 1	to 97
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The results obtained corroborated that both proteins are mostly disordered in solution over a wide range of temperatures (Fig. 2, A and B) and pH (data not shown), with the characteristic negative band for random coil structures around 198 nm.
Protein: DP01299 (UniProt Q96273)
Region: residues 1	to 97
Annotation: protein stabilization (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
For this purpose, LDH in the presence or absence of AtLEA4-5, AtLEA4-2, AtLEA4-51–77, or AtLEA4-578–158 was subjected to in vitro freeze-thaw cycles and partial dehydration treatments.
AtLEA4-2, the smallest protein of this group, mostly consisting of the N-terminal region (Fig. 1A), showed a similar protective effect on LDH activity as AtLEA4-5 after partial dehydration (Fig. 5A).
Protein: DP01299 (UniProt Q96273)
Region: residues 1	to 97
Annotation: cold acclimation (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
For this purpose, LDH in the presence or absence of AtLEA4-5, AtLEA4-2, AtLEA4-51–77, or AtLEA4-578–158 was subjected to in vitro freeze-thaw cycles and partial dehydration treatments.
AtLEA4-2, the smallest protein of this group, mostly consisting of the N-terminal region (Fig. 1A), showed a similar protective effect on LDH activity as AtLEA4-5 after partial dehydration (Fig. 5A).
Protein: DP01300 (UniProt Q9SLJ2)
Region: residues 1	to 98
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
the CD analysis indicated that the recombinant AtHIRD11 was disordered because the large negative peak around 200 nm occurred
Protein: DP01303 (UniProt O14519)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Full-length CDK2AP1 was analyzed by HDX-MS. The backbone amide groups in the entire N-terminal 60 residues of the protein exhibit rapid HDX rates characteristic of intrinsically disordered polypeptide segments
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of the NgBR ectodomain owned the largest negative signal at 198 nm and had no positive signal at 190 nm, indicating that it was predominantly unstructured.
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
It is highly possible that the NgBR cytoplasmic domain becomes well-folded upon binding isoprenyl lipids and/or prenylated proteins.
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
No significant difference was detected for its near-UV CD spectra in the absence and presence of 8 M urea , suggesting that the no tight tertiary packing existed in the NgBR ectodomain.
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder to order (Structural transition)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
It is highly possible that the NgBR cytoplasmic domain becomes well-folded upon binding isoprenyl lipids and/or prenylated proteins.
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
1H–15N NMR HSQC spectrum of the NgBR ectodomain displayed very narrow spectral dispersions over both dimensions (∼0.75 ppm for 1H and ∼20 ppm for 15N) as well as NMR resonance peaks could be observed for almost all residues. These characteristics indicated that the NgBR ectodomain is highly disordered in the free state
Protein: DP01304 (UniProt Q99LJ8)
Region: residues 47	to 120
Annotation: disorder to order (Structural transition)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
It is highly possible that the NgBR cytoplasmic domain becomes well-folded upon binding isoprenyl lipids and/or prenylated proteins.
Protein: DP01305 (UniProt P08392)
Region: residues 258	to 286
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Within the X-ray crystallography derived maps, electron
density was not observed for ICP4 residues 258–286, a region
previously predicted to be disordered, with the possible
exception of F283 and T284 in chain
Cross-references: PDB:5MHK
Protein: DP01305 (UniProt P08392)
Region: residues 258	to 289
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of 3D TOCSY-HSQC and NOESY-HSQC spectra allowed the amino acid type of 34 sharp backbone amide signals to be determined based on comparison with typical random coil chemical shifts. It was also possible to assign backbone amides to 21 residues within the N-terminal region 259–289, plus the C-terminal residues 485–487 (Figure 4E). While the remaining 10 peaks could not be attributed to specific sequence positions, their sidechain chemical shifts in the TOCSY spectra were characteristic of five arginines and five alanines, which matched the numbers of remaining unassigned residues scattered within regions 258–289 and 482–487.
1H-15N correlation NMR spectra acquired on ICP4NΔIDR contained broad and dispersed amide signals characteristic for a large globular protein, whereas in the longer ICP4N construct, we observed additional prominent sharp, poorly dispersed amide signals characteristic of the presence of an IDR
Cross-references: BMRB:26957
Protein: DP01305 (UniProt P08392)
Region: residues 258	to 287
Annotation: DNA binding (Molecular function)
Evidence: electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
These results suggest that an absolute requirement for tight specific binding is the presence of the intrinsically disordered N-terminal region, whereas if this region is deleted, the affinity for DNA consensus sequence is not only reduced, but approximately half of this consensus sequence is no longer recognized.
Protein: DP01305 (UniProt P08392)
Region: residues 258	to 289
Annotation: flexible linker (Disorder function)
Evidence: electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
The combination of the ICP4N globular homo-dimer and IDRs tune the specificity and maximize affinity for a DNA motif. Conversely, the combination of the IDRs with the apparent conformational plasticity of the S-loop and R-turn likely allows non-consensus DNA interactions with ICP4. The flexibility of these regions may facilitate the linear movement of ICP4 along a DNA duplex in search of high affinity consensus sites, or hopping along longer distances mediated by the IDRs.
Protein: DP01306 (UniProt Q03518)
Region: residues 1	to 112
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No density was observed for either the C-terminal 33 residues of ICP47 or the two TMD0s, indicating these regions are flexible in this conformation.
Cross-references: PDB:5U1D
Protein: DP01308 (UniProt O60828)
Region: residues 82	to 265
Annotation: disorder (Structural state)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
In the five constructs, the IDRs with average diameter 0.5 ± 0.1–0.3 nm (mean ± s.d.) appeared constantly disordered.
This Flory exponent ν is close to 0.5, which holds for 2D and three-dimensional (3D) ideal and Gaussian chains, indicating that these constantly disordered segments have similar values of persistence length (Lp)
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: pre-molten globule (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Incubation of PQBP-1 with ANS in the native condition (PBS) results in a blue shift of the fluorescence spectral peak from 510 nm to 475 nm accompanied by a threefold increase in quantum yield (Fig. 4 a). These effects are characteristic of ANS binding to a species adopting a premolten or molten-globule conformation. The relatively small increase in quantum yield suggested that ANS binding to PQBP-1 is not hydrophobic but instead is electrostatic in nature (43).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: pre-molten globule (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The RS of PQBP-1 obtained from gel filtration (3.50 nm) agrees well with that determined from sedimentation velocity experiments (3.67 nm), and that predicted for a natively disordered premolten globule protein (3.70 ± 0.41 nm).
The major peak has an elution volume that corresponds to two times the molecular mass of PQBP-1 (30.6 kDa), suggesting that the protein is dimeric if it adopts a compact, globular conformation. However, it is well established that elongated or unfolded proteins elute at a volume corresponding to a higher apparent molecular mass (40).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: pre-molten globule (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The RS of PQBP-1 obtained from gel filtration (3.50 nm) agrees well with that determined from sedimentation velocity experiments (3.67 nm), and that predicted for a natively disordered premolten globule protein (3.70 ± 0.41 nm).
The frictional coefficient ratio (f/f0) has a value of 1.74 (±0.09), which suggests that PQBP-1 is highly elongated. The Stokes radius of PQBP-1 calculated from these experiments is 3.67 (±0.02) nm.
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of PQBP-1 (Fig. 3 a) is typical of a protein or peptide without regular conformation: it lacks spectral features or any positive signals in the far-UV range, and has a characteristic negative maximum at 200 nm (41, 42). The absence of a positive CD signal below 200 nm indicates that there is very little or no helical structure.
From the top 20 solutions (data not shown), the spectrum is found to consist of a significant amount of β-strand structure (∼20–50%) and turns (∼15–40%), but little helical content (∼5–10%). The remaining regions of the protein (∼25–55%) are irregular structures. The variable temperature CD results are also typical of a disordered protein, with a broad melting profile (Fig. 3 b).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: pre-molten globule (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The processed scattering pattern of PQBP-1 (Fig. 5 a) yields an Rg of 3.8 (±0.2) nm, with a molecular mass of 30 (±3) kDa, suggesting that the protein remains monomeric in solution. The ratio of the Rg to the hydrodynamics radius (determined by AUC and SEC) is an indicator of the compactness of a protein. PQBP-1 has an Rg/RS ratio of 1.0, which is intermediate between the value of a spherical species (0.8) and that of an unstructured random coil (1.5) (47). 
Instead, this plot shows a peak at approximately q = 1 nm−1 followed by a shallow downward slope, suggesting that PQBP-1 is partially unfolded. The p(r) function of PQBP-1 has an asymmetric shape (Fig. 5 c), with its maximum at low r followed by a long tail. This is again consistent with an extended, perhaps partially unfolded molecule with the maximum dimension (Dmax) equal to 13 nm.
Protein: DP01308 (UniProt O60828)
Region: residues 223	to 265
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The N-terminal deletion mutants used were PQBP-1(179–265), PQBP-1(193–265) and PQBP-1(223–265). Fig. 2 shows that all of the deletion mutants bound to U5-15kD, and thus the residues 223 to 265 of PQBP-1 appear to be sufficient for the interaction with U5-15kD. The fragment PQBP-1(223–265) is called PQBP-1-CT43 in the following.
Protein: DP01308 (UniProt O60828)
Region: residues 223	to 265
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The attenuated resonances upon binding of PQBP-1-CT43 originate from residues in the α1 helix, the loop β2–β3, the strand β3, the loop β3–β4, and the strand β4 (Fig. 5A). These residues are located on one face of U5-15kD (Fig. 5B).
The HSQC spectrum of PQBP-1-CT43 in the free form is typical of an unstructured protein (Fig. 6A), since the backbone resonances are clustered together in a limited frequency range, spanning less than 0.7 ppm in the 1H dimension [23].
The binding of U5-15kD results in strong attenuation of the resonances originating from residues 241 to 263 of PQBP-1-CT43. From this, we conclude that the binding site is a continuous segment of residues 241–263 within the C-terminal domain, and that this segment undergoes some conformational and dynamical changes upon binding to U5-15kD.
On the other hand, there was no significant chemical shift change in residues 193–240 of PQBP-1 following the binding to U5-15kD [12]. This means that the residues 193–240, that is, the C-terminal domain except for the binding segment, remains unstructured even in the bound state.
Protein: DP01308 (UniProt O60828)
Region: residues 223	to 265
Annotation: protein binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The alanine substitutions markedly reduced the binding activity in the case of Y245A, V251A and L252A (Fig. 7). On the other hand, the N255A and R260A mutations slightly reduced the binding activity, although the effect of R260A was very small.
Protein: DP01308 (UniProt O60828)
Region: residues 220	to 265
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Next, we compared the 1H–15N HSQC spectra of the segmentally isotope-labeled PQBP1 and the isolated C-fragment of residues 220–265. The 1H–15N HSQC spectrum of the C-fragment shows the backbone amide resonances within 8.0–8.6 ppm in the 1H dimension (Fig. 3c). The narrow chemical shift dispersion in the 1H dimension is characteristic of IDPs
The 1H–15N HSQC spectrum of the segmentally isotope-labeled PQBP1 is similar to that of the C-fragment, and thus the C-segment (residues 220–265) within full-length PQBP1 is disordered like the isolated C-fragment (Fig. 3).
We concluded that the C-segment (residues 220–265) interacts very weakly with the N-segment (residues 1–220) within the context of full-length PQBP1. This is compatible with the solution model of PQBP1 reported by Ree et al. [42].
Protein: DP01308 (UniProt O60828)
Region: residues 238	to 260
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The refined model of the PQBP1-CT43 in the complex consists of the residues 238–260: it lacks the 15 N-terminal residues (residues 223–237; KRNEAKTGADTTAAG) and the 5 C-terminal residues (residues 261–265; TKQQD) owing to conformational flexibility (Fig. 2a). PQBP1-CT43 in the complex adopts an L-shaped structure with an extended conformation (residues 238–247) followed by an α-helix conformation (residues 248–259). The α-helix starts at Pro248, which generates the bend of the L-shaped structure.
Cross-references: PDB:4BWS
PDB:4BWQ
PDB:4CDO
Protein: DP01308 (UniProt O60828)
Region: residues 223	to 243
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of the fusion protein was refined to a resolution of 2.5 Å with an Rwork/Rfree value of 19/24% (Table 1). The refined model of the fusion protein is missing the residues 223–243 and 260–265 of PQBP1, presumably owing to conformational flexibility.
Cross-references: PDB:4BWS
PDB:4BWQ
PDB:4CDO