LiteFold/DisProt huggingface dataset:
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 117	to 350
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The IDD spectrum is quite different: the single negative maximum at 200 nm indicates that this domain contains long completely unfolded regions, and moreover, the overall low signal intensity suggests that β-strands are present in insignificant amounts judging from the form of the curve [32], [33].
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 117	to 350
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The spectrum of tryptophan fluorescence of the wt coilin has a peak at 347 nm, indicating both the hydrophilic environment of the tryptophan side chains and the poor formation of a globular hydrophobic core in the protein molecule. The central and C-terminal domains of coilin have fluorescence maxima at 350 nm for IDD and 354 nm for CTD, which indicates an even greater level of hydrophilicity in the local tryptophan environment.
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 212	to 350
Annotation: U2 snRNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In this report we have tested the ability of coilin to directly interact with two snRNAs - U2 snRNA and U1 snRNA and a non-specific artificial RNA (160 nt).
In contrast, the IDD complexes with RNA enter into the agarose gel. In this case no free RNA remains in the gel at the protein:RNA molar ratio 2[ratio]1. Further addition of the protein gradually increases retardation of the complex. The apparent Kd (0.04 µM) is lower than that of the wt protein (Figure 3A). These results suggest that coilin has at least two RNA-binding sites.
The distal part of IDD (IDD-212-350) provides RNA binding similar to that of the intact IDD with a Kd of 0.06 uM (Figure 3A, ​,4C). Interestingly, the C-terminus of IDD (IDD-282-350) shows no ability to bind RNA (Figure 3A, ​,4C). Consequently the NLS2 plays a main role as an RNA-binding cluster.
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 212	to 350
Annotation: U1 snRNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In this report we have tested the ability of coilin to directly interact with two snRNAs - U2 snRNA and U1 snRNA and a non-specific artificial RNA (160 nt).
In contrast, the IDD complexes with RNA enter into the agarose gel. In this case no free RNA remains in the gel at the protein:RNA molar ratio 2[ratio]1. Further addition of the protein gradually increases retardation of the complex. The apparent Kd (0.04 µM) is lower than that of the wt protein (Figure 3A). These results suggest that coilin has at least two RNA-binding sites.
The distal part of IDD (IDD-212-350) provides RNA binding similar to that of the intact IDD with a Kd of 0.06 uM (Figure 3A, ​,4C). Interestingly, the C-terminus of IDD (IDD-282-350) shows no ability to bind RNA (Figure 3A, ​,4C). Consequently the NLS2 plays a main role as an RNA-binding cluster.
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 212	to 350
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In this report we have tested the ability of coilin to directly interact with two snRNAs - U2 snRNA and U1 snRNA and a non-specific artificial RNA (160 nt).
In contrast, the IDD complexes with RNA enter into the agarose gel. In this case no free RNA remains in the gel at the protein:RNA molar ratio 2[ratio]1. Further addition of the protein gradually increases retardation of the complex. The apparent Kd (0.04 µM) is lower than that of the wt protein (Figure 3A). These results suggest that coilin has at least two RNA-binding sites.
The distal part of IDD (IDD-212-350) provides RNA binding similar to that of the intact IDD with a Kd of 0.06 uM (Figure 3A, ​,4C). Interestingly, the C-terminus of IDD (IDD-282-350) shows no ability to bind RNA (Figure 3A, ​,4C). Consequently the NLS2 plays a main role as an RNA-binding cluster.
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 350	to 409
Annotation: disorder (Structural state)
Evidence: author inference used in manual assertion
Supporting statements:
Using bioinformatic predictions of coilin structure, we suggest that Atcoilin contains two structural domains in the N-terminal part including an ordered domain on the N terminus (NOD) and a central internal disordered domain (IDD) and at least one domain in the C-terminal part (C-terminal domain, CTD) with a presumable Tudor-like structure abutting an intrinsically disordered C-terminus (Figure 1A).
The shift of a negative peak from 208 nm (which is characteristic for α-proteins) to 200 nm demonstrates that alongside the ordered secondary structure elements, the C-terminal domain also contains substantial unfolded regions, which likely correspond to the big loops between elements of the Tudor-like domain and also the long unfolded C-terminus.
All these residues are localized in unfolded regions of the CTD: one is within a loop between the Tudor fold β-sheets, two are more upstream, and the remainder is in the disordered extreme C-terminus.
The biophysical analysis assessed by circular dichroism and tryptophan fluorescence supports this region is disordered. Their combination with the the bioinformatic studies allows the authors to state that the CTD (350-608) contains a high degree of disorder interrupted by Tudor-like structured region (410-510).
Protein: DP02248 (UniProt Q8RWK8)
Region: residues 511	to 608
Annotation: disorder (Structural state)
Evidence: author inference used in manual assertion
Supporting statements:
Using bioinformatic predictions of coilin structure, we suggest that Atcoilin contains two structural domains in the N-terminal part including an ordered domain on the N terminus (NOD) and a central internal disordered domain (IDD) and at least one domain in the C-terminal part (C-terminal domain, CTD) with a presumable Tudor-like structure abutting an intrinsically disordered C-terminus (Figure 1A).
The shift of a negative peak from 208 nm (which is characteristic for α-proteins) to 200 nm demonstrates that alongside the ordered secondary structure elements, the C-terminal domain also contains substantial unfolded regions, which likely correspond to the big loops between elements of the Tudor-like domain and also the long unfolded C-terminus.
All these residues are localized in unfolded regions of the CTD: one is within a loop between the Tudor fold β-sheets, two are more upstream, and the remainder is in the disordered extreme C-terminus.
The biophysical analysis assessed by circular dichroism and tryptophan fluorescence supports this region is disordered. Their combination with the the bioinformatic studies allows the authors to state that the CTD (350-608) contains a high degree of disorder interrupted by Tudor-like structured region (410-510).
Protein: DP02249 (UniProt P38862)
Region: residues 618	to 630
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Truncation and mutagenesis analyses clearly showed that the binding affinity of Atg7 for Atg8 is predominantly provided by the C-terminal tail of ECTD, especially by residues 618–630, which were observed in our NMR structure but disordered in the crystal structure.
Protein: DP02249 (UniProt P38862)
Region: residues 618	to 630
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Truncation and mutagenesis analyses clearly showed that the binding affinity of Atg7 for Atg8 is predominantly provided by the C-terminal tail of ECTD, especially by residues 618–630, which were observed in our NMR structure but disordered in the crystal structure.
Protein: DP02251 (UniProt P68363)
Region: residues 416	to 447
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The rms deviations of backbone and all heavy atoms over residues 212–281 of the CAP-Gly-2 domain and residues 448–451 of the peptide are 0.13 and 0.51 Å, respectively. The rest of the peptide residues are disordered even in complex with the CAP-Gly-2 domain.
Cross-references: pdb:2e4h
Protein: DP02253 (UniProt Q96F86)
Region: residues 203	to 258
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal region encompassing the FDF motif (amino acids 203 to 258) is disordered.
Cross-references: PDB:3D3J
Protein: DP02253 (UniProt Q96F86)
Region: residues 203	to 258
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Co-crystalisation with the human DDX6 C-terminal domain.
Cross-references: imex:IM-23318-24635
Protein: DP02254 (UniProt P14598)
Region: residues 213	to 228
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The SH3A-SH3B linker is disordered in one of the molecules in the asymmetric unit.
Cross-references: PDB:1NG2
Protein: DP02254 (UniProt P14598)
Region: residues 213	to 228
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, the linker region (residues 213-228) had different NOE intensities in the free and complex forms. In the free state, the linker region showed negative NOE intensities (Fig. 3a), indicating that this region is highly flexible.
Whereas both SH3 domains form well defined structural cores, the linker region is moderately disordered due to a lack of long-range NOEs, consistent with the smaller hetNOE intensities (Fig. 3b).
Cross-references: PDB:1WLP
Protein: DP02254 (UniProt P14598)
Region: residues 296	to 330
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism studies show that peptide1 exists as a random coil in solution and does not have the same degree of helical structure as present in the auto-inhibited complex (data not shown).
The authors have previously specified that peptide 1 corresponds to residues 296-330.
Protein: DP02254 (UniProt P14598)
Region: residues 296	to 330
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Circular dichroism studies show that peptide1 exists as a random coil in solution and does not have the same degree of helical structure as present in the auto-inhibited complex (data not shown). This suggests that the low affinity of this interaction is a consequence of formation of secondary structure for which an energetic penalty has to be paid. This interpretation is supported by our ITC studies that show that this interaction is entropically unfavored and entirely driven by the enthalpic contribution.
Cross-references: PDB:1NG2
Protein: DP02254 (UniProt P14598)
Region: residues 296	to 330
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structure reveals an unexpected mode of target recognition by SH3 domains in which the conserved ligand binding surfaces of both SH3 domains are juxtaposed so as to create a single binding groove that is occupied by the N-terminal portion of the polybasic region (Figures 2A and 2B).
After exiting the conserved, tandem SH3 domain binding groove the remainder of the polybasic region changes its direction to run along SH3A and make extensive contacts with this domain and the N-terminal portion of the SH3A-SH3B linker. This is followed by another turn that allows residues 310–330 to run across both SH3 domains, approximately parallel to the SH3A-SH3B linker.
Cross-references: PDB:1NG2
Protein: DP02254 (UniProt P14598)
Region: residues 296	to 330
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We measured the binding affinity of the tandem SH3 domains, as well as the individual SH3 domains to a 35-mer peptide comprising residues 296–330 of the polybasic region (peptide1) by isothermal titration calorimetry (ITC). Binding of this peptide to either of the isolated SH3 domains (termed SH3A and SH3B) was undetectable under the experimental conditions, while the tandem SH3 domains bound with a Kd of 1.5 μM and a 1:1 stoichiometry (Figure 1B).
Protein: DP02254 (UniProt P14598)
Region: residues 296	to 304
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The additional interactions between the tandem SH3 domains and the C-terminal portion of the polybasic region, outside of the conserved binding groove, are crucial for the auto-inhibited conformation as evidenced by the low affinity of 29 μM of a peptide comprising residues 296–304 (peptide 2) for the tandem SH3 domains (Figure 1B).
The authors refer back to Figure 1B which shows ITC data with measured affinities.
Protein: DP02254 (UniProt P14598)
Region: residues 343	to 390
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
This model of truncated p47phox was then used as starting point for the fit of the experimental SAXS pattern of the full-length p47phox protein (Fig. 6B and Table S4), resulting in a set of full-length models carrying a mainly unstructured C-terminal part.
Protein: DP02254 (UniProt P14598)
Region: residues 343	to 390
Annotation: protein binding (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
The co-expression of p47phoxΔCter-CFP with p67phox-YFP gives clearly different FLIM images as compared with p47phox-CFP, with well-separated average lifetime distributions (Fig. 4, A and B), and measured Eapp values in the range of the first negative control (Fig. 4C and Fig. S3A). The observation of a plateau value for Eapp, well above the values of the controls, provides strong evidence for a specific interaction (17). The absence of significant FRET in the case of p47phoxΔCter shows in addition that the PRR domain of p47phox is required for this interaction in live cells.
We co-expressed p40phox and p47phox or its truncated version p47phoxΔCter with NC or CC labeling (Fig. 4, E and H). We found specific FRET in both cases with equivalent Eapp, which indicates that the FP tags at both termini of p40phox have a similar average geometry relative to the C terminus of p47phox. When p47phoxΔCter was used instead of full-length p47phox, no significant FRET was observed (Fig. 4E and Fig. S3C). This confirms the requirement of the PRR domain of p47phox for the interaction with p40phox in live cells.
Protein: DP02254 (UniProt P14598)
Region: residues 343	to 390
Annotation: protein binding (Molecular function)
Evidence: fluorescence correlation spectroscopy evidence
Supporting statements:
To evaluate independently the occurrence of an interaction between p47phox and p67phox tagged at their N termini, we used FCCS. In this technique, the fluctuations of the fluorescence intensities of FP-tagged p47phox and p67phox diffusing in and out a confocal volume in the cytosol of COS7 cells are analyzed by auto- and cross-correlation functions (see “Experimental procedures”). A cross-correlation function with a non-null amplitude was observed for p47phox and p67phox tagged either at their CC and NN termini (Fig. 5A), showing in both cases a co-diffusion of the fluorophores indicative of complex formation.
Protein: DP02254 (UniProt P14598)
Region: residues 213	to 228
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
However, the linker region (residues 213-228) had different NOE intensities in the free and complex forms. In the free state, the linker region showed negative NOE intensities (Fig. 3a), indicating that this region is highly flexible.
Whereas both SH3 domains form well defined structural cores, the linker region is moderately disordered due to a lack of long-range NOEs, consistent with the smaller hetNOE intensities (Fig. 3b). forms.
Cross-references: PDB:1WLP
Protein: DP02254 (UniProt P14598)
Region: residues 343	to 390
Annotation: flexible C-terminal tail (Disorder function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
This model of truncated p47phox was then used as starting point for the fit of the experimental SAXS pattern of the full-length p47phox protein (Fig. 6B and Table S4), resulting in a set of full-length models carrying a mainly unstructured C-terminal part.
Protein: DP02256 (UniProt P26554)
Region: residues 141	to 151
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The calculated structural ensemble (Figure 3a) exhibits a backbone r.m.s.d. of 0.62 Å for the structured 51Z2 region (residues 80 to 140 of the full length E6) while the backbone r.m.s.d. drops to 2.37 Å when including the less ordered E6 C-terminus (residues 141–151, numbering according to full-length sequence). This C-terminus gave rise to only few NOEs consistent with a less ordered organization.
Cross-references: BMRB:18967
PDB:2M3L
Protein: DP02256 (UniProt P26554)
Region: residues 141	to 151
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An interaction is observed, as several chemical shifts of amide groups arising from the C-terminus of 51Z2 were perturbed in presence of hDlgPDZ2 (Figure 4a). Surprisingly, the perturbation affected the C-terminal nine E6 residues (143 to 151), more than anticipated from either the canonical PDZ-BM or from the already published hDlgPDZ2-E6 peptide complex structures [52], [53]. Importantly, no further E6 resonances experienced chemical shift perturbation, clearly indicating that the interaction with the hDlgPDZ2 is confined to the disordered C-terminal region harboring the PDZ-BM of HPV51 E6.
The malleability of E6 is reminiscent of intrinsically disordered proteins that undergo a disorder-to-order transition upon productive complex formation with specific ligands [67].
Cross-references: PDB:2M3M
Protein: DP02256 (UniProt P26554)
Region: residues 141	to 151
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An interaction is observed, as several chemical shifts of amide groups arising from the C-terminus of 51Z2 were perturbed in presence of hDlgPDZ2 (Figure 4a). Surprisingly, the perturbation affected the C-terminal nine E6 residues (143 to 151), more than anticipated from either the canonical PDZ-BM or from the already published hDlgPDZ2-E6 peptide complex structures [52], [53]. Importantly, no further E6 resonances experienced chemical shift perturbation, clearly indicating that the interaction with the hDlgPDZ2 is confined to the disordered C-terminal region harboring the PDZ-BM of HPV51 E6.
Cross-references: PDB:2M3M
Protein: DP02256 (UniProt P26554)
Region: residues 141	to 151
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
The SPR data indicate a contribution to binding of the additional residues as the E6CT11 binds with higher affinity to hDlgPDZ2 than the E6CT6 (Kd 9.6 µM versus 28.3 µM, respectively; Figure 5).
Protein: DP02256 (UniProt P26554)
Region: residues 141	to 151
Annotation: regulation of proteolysis (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
An interaction is observed, as several chemical shifts of amide groups arising from the C-terminus of 51Z2 were perturbed in presence of hDlgPDZ2 (Figure 4a). Surprisingly, the perturbation affected the C-terminal nine E6 residues (143 to 151), more than anticipated from either the canonical PDZ-BM or from the already published hDlgPDZ2-E6 peptide complex structures [52], [53]. Importantly, no further E6 resonances experienced chemical shift perturbation, clearly indicating that the interaction with the hDlgPDZ2 is confined to the disordered C-terminal region harboring the PDZ-BM of HPV51 E6.
Cross-references: PDB:2M3M
Protein: DP02258 (UniProt Q9JLC3)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Both N-terminal (amino acids 1–18) and C-terminal (amino acids 105–116) regions are flexible ... This observation is consistent with the 15N-{H} NOE and 15N backbone relaxation data.
Cross-references: PDB:2KV1
Protein: DP02258 (UniProt Q9JLC3)
Region: residues 31	to 44
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A more disordered region, consisting of 13 residues (amino acids 31–44) between beta2- and beta3-strands, connects front side and back side beta-sheets of the protein.
Cross-references: PDB:2KV1
Protein: DP02258 (UniProt Q9JLC3)
Region: residues 105	to 116
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Both N-terminal (amino acids 1–18) and C-terminal (amino acids 105–116) regions are flexible ... This observation is consistent with the 15N-{H} NOE and 15N backbone relaxation data.
Cross-references: PDB:2KV1
Protein: DP02261 (UniProt P13848)
Region: residues 79	to 98
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The terminal 15 residues are disordered
The authors refers to the 80-98 region of this Uniprot, which has an extra methionine as a first residue, unlike the peptide they assessed.
Cross-references: PDB:1NO4
Protein: DP02261 (UniProt P13848)
Region: residues 80	to 98
Annotation: virion assembly (Biological process)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
In the first of these mutants the disordered C-terminal, residues 79-97 were deleted (Δ79-97 mutant), and in the second mutant residues 62-97, which comprises the last three helical turns of helix 3, were deleted. Both C-terminal deletions abolished the assembly activity (Fig 6).
The authors refers to the 80-98 region of this Uniprot, which has an extra methionine as a first residue, unlike the peptide they assessed.
Protein: DP02261 (UniProt P13848)
Region: residues 79	to 98
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The terminal 15 residues are disordered.
The PDBs show the protein lacks electron density starting from the residue 79 when assessed by X-ray.
Cross-references: PDB:1NOH
PDB:1NO4
Protein: DP02262 (UniProt P42226)
Region: residues 783	to 814
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H,15N-HSQC spectrum of 15N-13C-labeled STAT6783–814 (SI Fig. 1) shows narrow dispersion of signals in both proton and nitrogen dimensions indicating that the peptide adopts an unstructured conformation in absence of the binding partner.