LiteFold/DisProt huggingface dataset:
Protein: DP00622 (UniProt P63045)
Region: residues 2	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues: Sb 25–93, Sx 188–259, Sn1 7–83 and Sn2 131–204 for complex I; Sb 28–96, Sx 189–261, Sn1 12–83 and Sn2 132–203 for complex II; Sb 26–94, Sx 186–259, Sn1 11–83 and Sn2 132–204 for complex III; 19 water molecules; 13 Sr2+ ions; and 7 MPD molecules.
The N-terminal region of synaptobrevin (Sb) not visible in the crystal structure spans residues 2-24 in chain A and 2-27 in chain B.
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 168
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The lack of upfield-shifted resonances associated with methyl protons and very little dispersion in the amide proton region of the 1D 1H spectrum of CHOP, shown in Fig. 2A, suggest that CHOP comprises very little globular structure. Analysis of 1H-15N HSQC spectrum of CHOP revealed well-resolved backbone amide resonances for 81 of the expected 168 backbone 1H-15N correlations, which fell between 7.0 and 8.8 ppm (Fig. 2B).
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 168
Annotation: regulation of transcription by RNA polymerase II (Biological process)
Evidence: quantitative reverse transcription polymerase chain reaction evidence used in manual assertion
Supporting statements:
Overexpression of full-length CHOP increased the amount of β-catenin reporter inhibition in the presence of CaSR activation (%inhibition of activity in 5 μM Ca2+: 78 ± 5 vs 60 ± 4, p<0.05, n=6, Fig.6D). Overexpression of CHOP101−168 in the presence of CaSR activation did not change the amount of inhibition of the β-catenin reporter (% inhibition: 56 ± 6 vs 60 ± 4, NS, n=6).
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 168
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
 The fact that this is not the case for CHOP suggests that Trp18, Trp23, and Trp64 are located in the relatively symmetric environment and/or relatively accessible to solvent, indicating they are located in relatively flexible region.
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 120
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
This hypothesis is supported by the red-shifted maximum of the intrinsic fluorescence, λmax=345 nm (Fig. 3B). In fact, it is known that a tryptophan emission maximum is highly dependent on the polarity of its environment. A tryptophan residue in a non-polar environment (i.e., buried inside a protein), has an emission maximum close to 320 nm, while in a polar environment (i.e., solvent exposed) it has an emission maximum close to 350 nm, so-called Stokes shift 41.
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 168
Annotation: pre-molten globule (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The elution peaks observed for full-length CHOP correspond to RS of 44.7 and 72.8 Å while CHOP101−168 peak correspond to 32.3 Å.
If the elution peaks of full-length CHOP and CHOP101−168 are attributed to pre-molten globules, then the corresponding molecular masses are 163.8 kDa and 48.7 kDa for CHOP and 21.8 kDa for the CHOP101−168.
Protein: DP00624 (UniProt P35638)
Region: residues 1	to 168
Annotation: identical protein binding (Molecular function)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Fitting of the AUC data of CHOP resulted in no distinct peaks because of the large range of species of apparently high molecular mass, suggesting multiple oligomeric forms (data not shown). Conversely, when AUC data of CHOP101−168 were evaluated by a continuous distribution c(S) Lamm equation model, two distinct peaks (1.13S and 2.20 S) were observed (Fig. 4C). Integrating the c(M) distribution, SEDFIT 46 estimated these two peaks with median values of 9.9 kDa, 23.4% of total population and 24.3 kDa, 68% of total population, respectively suggesting a large population of apparent dimer and a small population of monomer. Altogether, these data suggest that when N-terminal region of CHOP is deleted, it can no longer make large oligomers.
Protein: DP00629 (UniProt Q07097)
Region: residues 443	to 524
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1DHN RDCs from the majority of the sequence follow the classically observed inverted bell-shaped distribution along the primary sequence, indicative of an unfolded peptide chain.
Protein: DP00629 (UniProt Q07097)
Region: residues 473	to 492
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR chemical shift titration studies of the NT:PX complex show that resonances of NT from throughout the interaction region (residues 473–492) experience line broadening (Figure S1, Supporting Information).
Protein: DP00629 (UniProt Q07097)
Region: residues 401	to 524
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
No detectable RD is measured in free NT (Figure S3, Supporting Information), confirming the rapid nature of the exchange between the three helical substates and the unfolded state.
Multinuclear RD provides an atomic resolution map of the molecular recognition trajectory of intrinsically disordered NT from the highly dynamic free-state equilibrium to the bound state, revealing a three-state interaction process whose binding modes and kinetics are regulated by the intrinsic dynamics of both proteins.
Protein: DP00629 (UniProt Q07097)
Region: residues 476	to 489
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Structural analysis of the different steps of NT binding to PX. (A) 13C′ secondary chemical shifts of the bound state of NT (derived by adding ΔωAB from the consensus three-state exchange model of Figure 4 to free-state shifts, red bars) and ASTEROIDS minimum ensemble selection against these shifts (blue line). A single ensemble substate, reporting on helix 476–489 populated to 100%, best reproduces the experimental data.
Protein: DP00629 (UniProt Q07097)
Region: residues 473	to 492
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR chemical shift titration studies of the NT:PX complex show that resonances of NT from throughout the interaction region (residues 473–492) experience line broadening (Figure S1, Supporting Information).
Protein: DP00629 (UniProt Q07097)
Region: residues 401	to 524
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We note that the backbone conformational propensities remain stable with temperature in the unfolded regions of NT, while the predominantly helical region (residues 476–492) shows a slight increase in helical propensity (around 5–7%) at lower temperatures as judged from temperature-corrected (80)13Cα chemical shifts (Figure S5).
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
While we observed complete broadening due to the increased relaxation around the spin-labeling sites, as would be expected for random coil ensembles, even residues distant in sequence from these sites exhibited significant PRE effects both in Sic1 and in pSic1.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1HN-15N correlation spectra (Fig. 1A) of Sic1 (black) and pSic1 (red) display limited amide proton chemical shift dispersion and sharp lines; such spectra are diagnostic of disordered proteins because the rapid interconversion of different conformers, many of which lack tertiary contacts, results in an averaged magnetic environment of the nuclei.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Titration of unlabeled Skp1–Cdc4 into a solution of 15N-labeled pSic1 allowed us to monitor the binding interaction by broadening of signals in NMR 1HN-15N correlation spectra.
The unaltered chemical shifts of the observable signals of pSic1 in the presence of Skp1–Cdc4 further demonstrate that pSic1 is disordered when in complex with Skp1–Cdc4.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
To obtain additional information on the molecular size distribution and the distribution of heavy atom distances in the ensembles, we collected SAXS data (Figure 2). The Kratky plots (Figure 2B) are typical for disordered protein states.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 284
Annotation: disorder (Structural state)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
Sic1-GFP exhibited a thin and flexible tail-like structure with a temporarily appearing and disappearing small globule at the N-terminal end, together with the C-terminal GFP. The R_2D histogram for the IDR was best fitted to a double Gaussian with peaks at 12.2 +/- 0.66 and 20.5 +/- 2.14 nm. The IDR is fully disordered in both shorter and longer states, as judged from its mean height of 0.4–0.5 nm in both metastable states 
The authors of the publication characterized an engineered fusion protein, i.e. recombinant Sic1 fused with GFP.
Protein: DP00631 (UniProt P38634)
Region: residues 31	to 190
Annotation: disorder to molten globule (Structural transition)
Evidence: atomic force microscopy evidence used in manual assertion
Supporting statements:
The large number around 190 indicates that as much as about 65% of the whole protein is loosely folded, with only the remaining C-terminal region (encompassing about 95aa) being fully extended. The remarkable difference between 30 and 190 indicates that a large segment containing about 160 residues undergoes a transition between fully unstructured and loosely folded conformations.
The authors of the publication characterized an engineered fusion protein, i.e. recombinant Sic1 fused with GFP.
Protein: DP00631 (UniProt P38634)
Region: residues 3	to 7
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 31	to 35
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 43	to 47
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 67	to 71
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 74	to 78
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 78	to 82
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The identity of phosphorylated residues was confirmed by NMR. The CDK sites at Thr5, Thr33, Thr45, Ser69, Ser76, and Ser80 were phosphorylated, whereas Thr2 was not phosphorylated in this construct.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: SCF ubiquitin ligase complex binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We next evaluated the interaction of 6-fold phosphorylated Sic1 with a monomeric Skp1–Cdc4 complex; the Skp1 subunit of SCFCdc4 is required for soluble expression of Cdc4 but does not interact with substrates (24). Using an intrinsic Trp fluorescence-binding assay, we measured an apparent overall Kd value of ≈0.6 μM between the pSic1 preparation and Skp1–Cdc4, whereas no binding was detected for Sic1.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We next evaluated the interaction of 6-fold phosphorylated Sic1 with a monomeric Skp1–Cdc4 complex; the Skp1 subunit of SCFCdc4 is required for soluble expression of Cdc4 but does not interact with substrates (24). Using an intrinsic Trp fluorescence-binding assay, we measured an apparent overall Kd value of ≈0.6 μM between the pSic1 preparation and Skp1–Cdc4, whereas no binding was detected for Sic1.
Protein: DP00631 (UniProt P38634)
Region: residues 1	to 90
Annotation: SCF ubiquitin ligase complex binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Titration of unlabeled Skp1–Cdc4 into a solution of 15N-labeled pSic1 allowed us to monitor the binding interaction by broadening of signals in NMR 1HN-15N correlation spectra. 
The unaltered chemical shifts of the observable signals of pSic1 in the presence of Skp1–Cdc4 further demonstrate that pSic1 is disordered when in complex with Skp1–Cdc4.
Protein: DP00633 (UniProt Q09472)
Region: residues 401	to 566
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, no folded structure could be detected in the IHD.
Protein: DP00633 (UniProt Q09472)
Region: residues 1	to 1045
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Evidently, significant parts of the unstructured regions at the N- and C-termini (∼650 amino acids, Figure 3A) were not visible in our reconstruction, likely because of the dynamic nature of those regions. Considering that the p300 map encompassed the structured core domain and partly other N- and C-terminal structured domains, the effective molecular mass was adequate. We concluded that, in free form, the central (core) domain of p300 stays in a closely compact conformation as seen in the crystal structure, while unstructured linkers and part of N- and C-terminal domains remains in an ensemble of assorted dynamic conformations.
Cross-references: PDB:6K4N
EMDB:6792
Protein: DP00633 (UniProt Q09472)
Region: residues 1665	to 2414
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Evidently, significant parts of the unstructured regions at the N- and C-termini (∼650 amino acids, Figure 3A) were not visible in our reconstruction, likely because of the dynamic nature of those regions. Considering that the p300 map encompassed the structured core domain and partly other N- and C-terminal structured domains, the effective molecular mass was adequate. We concluded that, in free form, the central (core) domain of p300 stays in a closely compact conformation as seen in the crystal structure, while unstructured linkers and part of N- and C-terminal domains remains in an ensemble of assorted dynamic conformations.
Cross-references: PDB:6K4N
EMDB:6792
Protein: DP00633 (UniProt Q09472)
Region: residues 1520	to 1581
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Evidently, significant parts of the unstructured regions at the N- and C-termini (∼650 amino acids, Figure 3A) were not visible in our reconstruction, likely because of the dynamic nature of those regions. Considering that the p300 map encompassed the structured core domain and partly other N- and C-terminal structured domains, the effective molecular mass was adequate. We concluded that, in free form, the central (core) domain of p300 stays in a closely compact conformation as seen in the crystal structure, while unstructured linkers and part of N- and C-terminal domains remains in an ensemble of assorted dynamic conformations.
Cross-references: PDB:6K4N
EMDB:6792
Protein: DP00633 (UniProt Q09472)
Region: residues 1520	to 1581
Annotation: order (Structural state)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
A model of the autoinhibitory loop was made (using PHYRE2 (50)), which could be accommodated in this loop density (Figure 4D).
Figure 4 shows this region is structured when the protein is in complex with p53.
Cross-references: EMDB:6791
PDB:5XZC
Protein: DP00633 (UniProt Q09472)
Region: residues 1520	to 1581
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
A model of the autoinhibitory loop was made (using PHYRE2 (50)), which could be accommodated in this loop density (Figure 4D).
While this region lacks electron density in the PDB structure 6K4N,  Figure 4 and PDB 5XZC shows this region is structured when the protein is in complex with p53.
Thus, our structural analyses illustrated that, while conformation of the p300 central (core) domain in free form can be considered as a “closed” configuration, in the complex with p53, it transformed to an “open” conformation.
Cross-references: EMDB:6791
PDB:5XZC
EMDB:6792
PDB:6K4N
Protein: DP00652 (UniProt P00441)
Region: residues 69	to 78
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 67–79 and 126–141 are disordered and not visible in the electron density.
The A4V variant is responsible for the majority of familial ALS cases in North America, causing rapidly progressing paralysis once symptoms begin and the G93A SOD1 variant is overexpressed in often studied murine models of the disease.
In the metal-free structures, the metal-binding loop elements are observed to be severely disordered, suggesting that these variants may share mechanisms of aggregation proposed previously for other pathogenic SOD1.
Authors refer to the Ala5Val substitution accordingly to the UniProt sequence.
Cross-references: PDB:3GZQ
Protein: DP00652 (UniProt P00441)
Region: residues 127	to 142
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 67–79 and 126–141 are disordered and not visible in the electron density.
The A4V variant is responsible for the majority of familial ALS cases in North America, causing rapidly progressing paralysis once symptoms begin and the G93A SOD1 variant is overexpressed in often studied murine models of the disease.
In the metal-free structures, the metal-binding loop elements are observed to be severely disordered, suggesting that these variants may share mechanisms of aggregation proposed previously for other pathogenic SOD1.
Authors refer to the Ala5Val substitution accordingly to the UniProt sequence.
Cross-references: PDB:3GZQ
Protein: DP00652 (UniProt P00441)
Region: residues 127	to 142
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The molecules of A4V and I113T mutant SOD1 pack into the crystals in a so-called “trimer-of-dimers” motif (Fig. 5, which is published as supporting information on the PNAS web site), involving primarily interactions between residues 128–131 of the electrostatic loop in one molecule and Thr-88, Ser-96, and Ser-98 from the Zn loop of a second SOD1 molecule.
The overall fold observed for wtSOD (12, 13, 34) is largely preserved in the A4V and I113T mutants.
When interacting with Cu+2 and Zn+2 ions, this region of the pathogenic variant (with the mutation Ala5Val, according to the UniProt sequence) is structured.
Cross-references: PDB:1UXM
Protein: DP00652 (UniProt P00441)
Region: residues 69	to 78
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The molecules of A4V and I113T mutant SOD1 pack into the crystals in a so-called “trimer-of-dimers” motif (Fig. 5, which is published as supporting information on the PNAS web site), involving primarily interactions between residues 128–131 of the electrostatic loop in one molecule and Thr-88, Ser-96, and Ser-98 from the Zn loop of a second SOD1 molecule.
The overall fold observed for wtSOD (12, 13, 34) is largely preserved in the A4V and I113T mutants.
When interacting with Cu+2 and Zn+2 ions, this region of the pathogenic variant (with the mutation Ala5Val, according to the UniProt sequence) is structured.
Cross-references: PDB:1UXM