LiteFold/DisProt huggingface dataset:
Protein: DP01489 (UniProt Q9UBK2)
Region: residues 2	to 220
Annotation: protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
PGC-1α and ERRγ share tissue specificity, have overlapping functions, and demonstrate a robust physical and functional interaction.
Protein: DP01489 (UniProt Q9UBK2)
Region: residues 2	to 220
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Kratky and Porod–Debye plots for the complex are indicative of a well-folded globular particle. Combined, these experiments indicate that PGC1α220 undergoes
a disorder-to-order transition upon docking onto the LBD, resulting in a binary complex, which is significantly more compact and structured.
Protein: DP01489 (UniProt Q9UBK2)
Region: residues 2	to 220
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD analysis of PGC1α220 estimated only 27% native secondary structure in the activation domain.
Protein: DP01490 (UniProt Q9NR61)
Region: residues 553	to 685
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of DLL4_IC in Tris buffer shows a strong minimum at 198 nm, which is typical of disordered proteins.
Protein: DP01490 (UniProt Q9NR61)
Region: residues 553	to 685
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The lack of chemical shift dispersion in the HN region as well as in the methyl region indicates the absence of globular structure, and the presence of little, if any, secondary structure.
Protein: DP01490 (UniProt Q9NR61)
Region: residues 553	to 685
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Delta-4 was shown to interact through its evolutionarily conserved C-terminal motif (ATEV) with the PDZ domains of Dlg-1, the human homologue of Drosophila Discs Large protein.
Protein: DP01490 (UniProt Q9NR61)
Region: residues 553	to 685
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
We interpret size exclusion chromatography results as indicative of the presence of a monomeric, disordered but partially compact state.
Protein: DP01491 (UniProt P22059)
Region: residues 346	to 379
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All residues of OSBPF showed negative NOE values in the unbound state, suggesting that free OSBPF is flexible. Structure analysis of free OSBPF using the TALOS program with the assigned 1HN, 15N, 13C, C, and 13C chemical shifts also showed no ordered structure.
Protein: DP01491 (UniProt P22059)
Region: residues 346	to 379
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Oxysterol-binding protein (OSBP), a cytosolic receptor of cholesterol and oxysterols, is recruited to the endoplasmic reticulum by binding to the cytoplasmic major sperm protein (MSP) domain of integral endoplasmic reticulum protein VAMP-associated protein-A (VAP-A).
Protein: DP01491 (UniProt P22059)
Region: residues 346	to 379
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to VAP-AMSP, 1H,15N hetero-NOE values of the residues around the FFAT motif of OSBPF changed from negative to positive, indicating that OSBPF formed a stable structure upon binding to VAP-AMSP.
Protein: DP01492 (UniProt Q01097)
Region: residues 1259	to 1482
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism of N2B showed no signs of secondary structure (Figure 4). This is the first experimental conformation that the cytoplasmic domain is disordered.
Protein: DP01492 (UniProt Q01097)
Region: residues 1259	to 1482
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited trypsin proteolysis of CTD2 with 2 μg/ml trypsin resulted in complete degradation in less than 30 min as expected for a disordered protein (Fig. 2B). High molecular weight intermediate bands are visible at early time points indicating that some cleavage sites are partially protected.
Protein: DP01492 (UniProt Q01097)
Region: residues 1259	to 1482
Annotation: disorder (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Although the constructs sample different regions of CTD2, there was little dispersion in the FRET peaks suggesting a lack of local structure.
Protein: DP01492 (UniProt Q01097)
Region: residues 1259	to 1482
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Analytical SEC of N2B gave an RH of 3.27 ± 0.021 nm for an apparent molecular weight of 70.4 ± 1.2 kDa compared with the actual molecular weight of 25.3 kDa.
Protein: DP01492 (UniProt Q01097)
Region: residues 1334	to 1338
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
The shift from phosphorylation was dependent on the presence of Mg2+ as Src in the presence of ATP alone had no effect. To confirm the sites of Src phosphorylation, we mutated Tyr-1336 and Tyr-1472 to threonine (ΔY), which eliminated the mobility shift induced by Src (right lanes, Fig. 2A).
Protein: DP01492 (UniProt Q01097)
Region: residues 1470	to 1474
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
The shift from phosphorylation was dependent on the presence of Mg2+ as Src in the presence of ATP alone had no effect. To confirm the sites of Src phosphorylation, we mutated Tyr-1336 and Tyr-1472 to threonine (ΔY), which eliminated the mobility shift induced by Src (right lanes, Fig. 2A).
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As expected, the spectra indicated that T-peptide is a random coil whereas both ABbt and HMGB1 are predominantly α-helical.
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The association constant determined by isothermal titration calorimetry (ITC) of T-peptide with box A was (1.1 ± 0.14) × 105 M-1 (KD = 9 μM) (Figure 3, trace C). The ITC tracings are typical for a weak interaction. The stoichiometry is close to 1:1. The interaction at 293 K is favorable both enthalpically (ΔHobs = −2.6 ± 0.15 kcal/mol) and entropically (TΔSobs = 4.2 kcal/mol). The negative binding enthalpy suggests the existence of favorable polar interactions.
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: self-assembly (Disorder function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The association constant determined by isothermal titration calorimetry (ITC) of T-peptide with box A was (1.1 ± 0.14) × 105 M-1 (KD = 9 μM) (Figure 3, trace C). The ITC tracings are typical for a weak interaction. The stoichiometry is close to 1:1. The interaction at 293 K is favorable both enthalpically (ΔHobs = −2.6 ± 0.15 kcal/mol) and entropically (TΔSobs = 4.2 kcal/mol). The negative binding enthalpy suggests the existence of favorable polar interactions.
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: self-assembly (Disorder function)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Sedimentation equilibrium experiments confirmed that the complex between box A and the T-peptide has a mass of16 ± 2 kDa, compatible with the formation of a strong 1:1 complex (data not shown).
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: protein binding (Molecular function)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
Sedimentation equilibrium experiments confirmed that the complex between box A and the T-peptide has a mass of16 ± 2 kDa, compatible with the formation of a strong 1:1 complex (data not shown).
Protein: DP01493 (UniProt P09429)
Region: residues 166	to 214
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure of the amino acids belonging to the basic region downstream of box B was assessed using Cα secondary chemical shifts and 15N NOESY-HSQC experiment. Both methods indicate that this amino acid stretch is unstructured:  ΔCα chemical shifts are negative and the NOEs typical of α-helices and β-sheets are absent (data not shown).
The residues in the acidic tail have typical random coil frequencies, with sharp and intense peaks. Individual tail residues could not be assigned:  the corresponding peaks are fewer than expected because of spectral overlap and exchange with the solvent.
HMG box A comprises approximately aa 4−80 (black), HMG box B aa 90−165 (dark gray), and the acidic tail aa 185−214 (gray). The linker between box A and box B is in white, and the basic stretch between box B and the tail is in light gray.
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift differences were small, suggesting that the conformational changes of the ABbt fragment upon binding of the T-peptide are small. This facilitated residue assignment in the complex. Most chemical shift changes were a continuous and monotonic function of the amount of added T-peptide (up to a 1:4 protein:peptide ratio), indicative of a fast-exchange regime on the NMR time scale. However, at substoichiometric ratios we observed line broadenings for the peaks corresponding to T76, I78, and I158, indicative of an intermediate exchange regime. The residues showing the largest ΔCS are T76 and I78 in box A and N92, A93, I158, and R162 in box B, as shown in the lower part of Figure 4. Several nearby residues (Y70, R72, and K81 in box A and A163, K164, and G165 in box B) are also affected to a lower extent.
The interaction of the T-peptide with box A reaches saturation at a stoichiometry of 3:1 (T-peptide:box A), whereas the interaction with box B does not reach saturation up to a 5-fold excess of T-peptide (data not shown). This result is in agreement with the ITC and thermostability data indicating that the interaction of the T-peptide with box B is much weaker than with box A.
Box A correspond to the 4-80 region and Box B to the 90-165 region of the protein.
Protein: DP01493 (UniProt P09429)
Region: residues 188	to 214
Annotation: self-assembly (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift differences were small, suggesting that the conformational changes of the ABbt fragment upon binding of the T-peptide are small. This facilitated residue assignment in the complex. Most chemical shift changes were a continuous and monotonic function of the amount of added T-peptide (up to a 1:4 protein:peptide ratio), indicative of a fast-exchange regime on the NMR time scale. However, at substoichiometric ratios we observed line broadenings for the peaks corresponding to T76, I78, and I158, indicative of an intermediate exchange regime. The residues showing the largest ΔCS are T76 and I78 in box A and N92, A93, I158, and R162 in box B, as shown in the lower part of Figure 4. Several nearby residues (Y70, R72, and K81 in box A and A163, K164, and G165 in box B) are also affected to a lower extent.
The interaction of the T-peptide with box A reaches saturation at a stoichiometry of 3:1 (T-peptide:box A), whereas the interaction with box B does not reach saturation up to a 5-fold excess of T-peptide (data not shown). This result is in agreement with the ITC and thermostability data indicating that the interaction of the T-peptide with box B is much weaker than with box A.
Box A correspond to the 4-80 region and Box B to the 90-165 region of the protein.
Protein: DP01494 (UniProt Q9VMA3)
Region: residues 340	to 361
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Cup interacts with eIF4E as two short a-helices connected
by a linker that is disordered in the structure.
Cross-references: PDB:4AXG
Protein: DP01494 (UniProt Q9VMA3)
Region: residues 340	to 361
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Cup interacts with eIF4E as two short a-helices connected
by a linker that is disordered in the structure.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H NMR spectrum of ShB-C lacks the chemical shift dispersion typical of folded proteins. Hence, our results suggest that the C-terminal portion of the Shaker channel is an intrinsically disordered random chain.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
His6-tagged ShB-C, immobilized on Ni2 beads via its N terminus, is able to capture PSD-95 from a crude soluble protein extract of transformed Drosophila Schneider cells.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum for ShB-C lacked the typical signatures of secondary structure. ShB-C exhibited a negative peak at 200
nm, indicative of a strong contribution from disordered structural elements, characteristic of a protein in a random coil
conformation.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Thus, we conclude that ShB-C behaves as a random coil with very low compactness. Dynamic light
scattering further supports this conclusion, yielding a Stokes radius of 37.2 Å.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: disorder (Structural state)
Evidence: near-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectrum in the near-UV range (250–330 nm) was devoid of any ellipticity (not shown), indicating the absence of
oriented aromatic residues typically present in the hydrophobic cores of compact globular proteins.
Protein: DP01495 (UniProt P08510)
Region: residues 513	to 655
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
ShB-C migrates in a size-exclusion column unusually fast for a 15.9-kDa protein. Thus, we conclude that ShB-C
behaves as a random coil with very low compactness.
Protein: DP01496 (UniProt P0AFG0)
Region: residues 117	to 131
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In PMID: 20413501 the same group states in the supplementary material based on this work: NusG-CTD (132-181; green; PDB ID: 2JVV; (16)) is connected
with the NTD via a flexible linker region (117-131)
Cross-references: PDB:2JVV
PDB:2K06
Protein: DP01496 (UniProt P0AFG0)
Region: residues 117	to 131
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This
observation suggests that (1) EcNusG consists of at
least two domains that are connected via a flexible
linker.
Protein: DP01496 (UniProt P0AFG0)
Region: residues 45	to 65
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The sequence region P45–F65 shows
chemical shifts typical for unstructured residues and no medium- or long-range nuclear Overhauser
enhancement cross signals for these residues were
observed, suggesting that this sequence region
forms a highly flexible loop.
Cross-references: PDB:2K06
Protein: DP01497 (UniProt Q9NK80)
Region: residues 750	to 956
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the 1D 1H-NMR spectrum of Gli-cyt in H2O, the chemical shifts are in the narrow range between 0.8 and 8.5 ppm, demonstrating that Gli-cyt exists in solution as a mixture of rapidly equilibrating extended conformers.
Protein: DP01497 (UniProt Q9NK80)
Region: residues 750	to 956
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The experimentally determined RST for Gli-cyt, 33.4 Å, is significantly larger than expected for either the native orMGstates. However, it is significantly lower than
expected for a random coil, suggesting that it may be in a PMG state.
Protein: DP01497 (UniProt Q9NK80)
Region: residues 750	to 956
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of Gli-cyt displays a maximum negative ellipticity at 200 nm and a low ellipticity at 222 nm, which are indicative of a strong contribution from disordered structural elements.
Protein: DP01498 (UniProt O70480)
Region: residues 47	to 117
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
SNARE motifs are unstructured in solution, but assume a helical conformation when they interact with each other. Using circular dichroism (CD, 220 nm) spectroscopy, we therefore investigated which of the possible combinations of early endosomal SNARE motifs result in increases in α‐helicity. As expected for SNARE core complexes, combination of all four SNARE motifs resulted in a major increase of α‐helical content.
Cross-references: pdb:2nps
Protein: DP01498 (UniProt O70480)
Region: residues 47	to 117
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The crystal structure of the early endosomal SNARE complex (composed of syntaxin 13, vti1a, syntaxin 6, and VAMP4) was solved and refined at a resolution of 2.7 Å. The overall structure revealed that the SNARE complex forms a four‐helix bundle with a left‐handed superhelical twist.
Cross-references: pdb:2nps
Protein: DP01498 (UniProt O70480)
Region: residues 47	to 117
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The combination of all four SNARE motifs (syntaxin 13, vti1a, syntaxin 6, and VAMP4) resulted in a major increase of α‐helical content.
Protein: DP01499 (UniProt Q9JI51)
Region: residues 115	to 192
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
SNARE motifs are unstructured in solution, but assume a helical conformation when they interact with each other. Using circular dichroism (CD, 220 nm) spectroscopy, we therefore investigated which of the possible combinations of early endosomal SNARE motifs result in increases in α‐helicity. As expected for SNARE core complexes, combination of all four SNARE motifs resulted in a major increase of α‐helical content.
Cross-references: pdb:2nps
Protein: DP01499 (UniProt Q9JI51)
Region: residues 115	to 192
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The crystal structure of the early endosomal SNARE complex (composed of syntaxin 13, vti1a, syntaxin 6, and VAMP4) was solved and refined at a resolution of 2.7 Å. The overall structure revealed that the SNARE complex forms a four‐helix bundle with a left‐handed superhelical twist.
Cross-references: pdb:2nps
Protein: DP01499 (UniProt Q9JI51)
Region: residues 115	to 192
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The combination of all four SNARE motifs (syntaxin 13, vti1a, syntaxin 6, and VAMP4) resulted in a major increase of α‐helical content.
Protein: DP01500 (UniProt Q5R6Q2)
Region: residues 169	to 232
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
SNARE motifs are unstructured in solution, but assume a helical conformation when they interact with each other. Using circular dichroism (CD, 220 nm) spectroscopy, we therefore investigated which of the possible combinations of early endosomal SNARE motifs result in increases in α‐helicity. As expected for SNARE core complexes, combination of all four SNARE motifs resulted in a major increase of α‐helical content.
Protein: DP01500 (UniProt Q5R6Q2)
Region: residues 169	to 232
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The crystal structure of the early endosomal SNARE complex (composed of syntaxin 13, vti1a, syntaxin 6, and VAMP4) was solved and refined at a resolution of 2.7 Å. The overall structure revealed that the SNARE complex forms a four‐helix bundle with a left‐handed superhelical twist.
Cross-references: pdb:2nps
Protein: DP01500 (UniProt Q5R6Q2)
Region: residues 169	to 232
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The combination of all four SNARE motifs (syntaxin 13, vti1a, syntaxin 6, and VAMP4) resulted in a major increase of α‐helical content.
Protein: DP01501 (UniProt G3V7P1)
Region: residues 182	to 250
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The crystal structure of the early endosomal SNARE complex (composed of syntaxin 13, vti1a, syntaxin 6, and VAMP4) was solved and refined at a resolution of 2.7 Å. The overall structure revealed that the SNARE complex forms a four‐helix bundle with a left‐handed superhelical twist.
Cross-references: pdb:2nps
Protein: DP01501 (UniProt G3V7P1)
Region: residues 182	to 250
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The combination of all four SNARE motifs (syntaxin 13, vti1a, syntaxin 6, and VAMP4) resulted in a major increase of α‐helical content.