LiteFold/DisProt huggingface dataset:
Protein: DP01175 (UniProt P28235)
Region: residues 233	to 333
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift index predictions of secondary structure and the lack of medium- and long-range NOE connectivities observed in the 1H–15N NOESY-HSQC and 1H-13C-NOESY spectra are consistent with the prediction of an intrinsically disordered structure for the Cx37CT.
Protein: DP01175 (UniProt P28235)
Region: residues 233	to 333
Annotation: molecular recognition display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The CT plays a role in the trafficking, localization, and turnover of gap junction channels, as well as the level of gap junction intercellular communication via numerous post-translational modifications and protein-protein interactions.
Protein: DP01175 (UniProt P28235)
Region: residues 233	to 333
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The CT plays a role in the trafficking, localization, and turnover of gap junction channels, as well as the level of gap junction intercellular communication via numerous post-translational modifications and protein-protein interactions.
Protein: DP01176 (UniProt P08033)
Region: residues 217	to 283
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of the 15N-NOESY spectra did not produce NOEs consistent with any secondary structure. The intrinsically disordered structure for the soluble Cx32CT domain as determined by CD is consistent with the narrow 1H chemical shift dispersions (<1 ppm) observed in the 15N-HSQC.
Protein: DP01176 (UniProt P08033)
Region: residues 217	to 283
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Cx32CT domain interacts with the protein partners synapse-associated protein 97 (SAP97) and calmodulin (CaM).
Protein: DP01176 (UniProt P08033)
Region: residues 217	to 283
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The soluble Cx32CT showed a peak minimum near 198 nm and little ellipticity at 222 nm, characteristic of a flexible, intrinsically disordered protein.
Protein: DP01176 (UniProt P08033)
Region: residues 217	to 283
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of the 15N-NOESY spectra did not produce NOEs consistent with any secondary structure. The intrinsically disordered structure for the soluble Cx32CT domain as determined by CD is consistent with the narrow 1H chemical shift dispersions (<1 ppm) observed in the 15N-HSQC.
Protein: DP01177 (UniProt P0AE98)
Region: residues 19	to 49
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The backbone and sidechain resonances were assigned using three-dimensional NMR spectra of the monomer, following standard procedures. Solely, the prolines, the C-terminal His6-tag and three residues at the N terminus remained unassigned. Eventually, 79% of protons and more than 69% of heteroatoms could be assigned. The structure was calculated with a total number of 1027 NOE restraints out of which 12% could be assigned to long range distance restraints. The structure of CsgF consists of three independent elements: An N-terminal unstructured region, a 21-residue a-Helix and a C-terminal antiparallel b-sheet made of four strands. Almost all long range restraints were found to deﬁne the b-sheet. The bundle of the lowest energy structures demonstrates that no unique arrangement between the three regions could be determined due to the absence of interdomain NOE restraints.
Cross-references: BMRB:34052
PDB:5m1u
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
Thermal stability is a key feature of mostly disordered proteins. Due to their specific amino acid composition and their inherent lack of structure, no aggregation occurs at high temperatures. According to our expectations, the level of intact hNopp140 has not changed after 10 min of boiling, while the globular control BSA aggregated and
precipitated.
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum of hNopp140 has a characteristic peak with a minimum at 203 nm tending to disappear at 220 nm. This resembles the CD spectrum of IDPs that are characterized with a minimum at 200 nm, and an approximately zero value at 220 nm.
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Previously it was shown that the phosphorylated form of hNopp140 preferentially binds to CK2, suppressing the catalytic activity of the enzyme. This enzyme is highly conserved in eukaryotes and is implicated in cell proliferation, apoptosis and differentiation. In fact, CK2 was found to be primarily responsible for extensive phosphorylation of hNopp140.
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Protease sensitivity is another important marker of disordered proteins, because their extended structure makes them fully accessible to the action of proteases. In accord, hNopp140 proved to be highly sensitive to proteolysis which is another piece of evidence underlining its disordered status. The level of intact BSA has hardly changed in the
time-scale used in our experiment, while hNopp140 was degraded promptly by both proteinase K and trypsin. After only 30 s there was practically no detectable hNopp140 left,while the level of BSA stayed stable even after 1 min
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As further evidence for the absence of folded structure, the proton 1D spectrum is concentrated to a relatively narrow ppm region. The reason for this is that the similar chemical environment of the protons in the same chemical group results in very similar chemical shifts. The proton 1D spectrum of globular proteins spreads over a much wider
range due to the very big differences in the local magnetic environments. 1H-NMR spectra of hNopp140 is characterized by line narrowing and lack of resonance dispersion typical of a disordered protein.
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: phosphorylation display site (Disorder function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Most serine residues are phosphorylated by casein kinase 2 (CK2), which makes hNopp140 one of the most highly phosphorylated proteins in the cell with approximately 80 phosphates per molecule. Several other kinases such as PKA, PKC and cdc2 kinase, are able to phosphorylate Nopp140 underlining the importance of the phosphorylation in the regulation of the function of the protein and it was also shown that PKA and not CK2 phosphorylation was necessary for the rat Nopp140 to be able to activate agp gene expression.
Protein: DP01178 (UniProt Q14978)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Protein disorder also manifests itself in other physical characteristics, such as aberrant mobility in gel filtration. Most IDPs elute at two to six times higher molecular weight than their actual size. The apparent molecular weight of hNopp140 extrapolated from the data of four protein standards is 511.0 kDa in contrast to the 75.58 kDa
calculated from its amino acid sequence, resulting in an apparent molar weight 7 times higher than the actual size of the molecule.
The hydrodynamic radius of hNopp140 was also determined in this
experiment and gave a result of 5.7 nm. Based on the classification of
unfolded proteins according to their compactness [42], hNopp140 falls
somewhere between random coil and premolten globule, but it is closer
to the latter category (Fig. 3B).
Protein: DP01180 (UniProt Q8RY59)
Region: residues 468	to 509
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H, 15N HSQC spectrum of RCD1 (468–589) is shown in Fig. 1b, in which the labels are colored according to this structure prediction. In agreement with the prediction, about half of the amide peaks, originating from the structured segment, are widely dispersed (green labels) and have uniform peak intensities while the other half are clustered in a narrow region of the 1HN axis and show great variance in peak intensities, ranging from very weak (e.g. V469–L471 and G491–S495) to very high (e.g. D476–L481).
Cross-references: BMRB:27034
Protein: DP01180 (UniProt Q8RY59)
Region: residues 568	to 589
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H, 15N HSQC spectrum of RCD1 (468–589) is shown in Fig. 1b, in which the labels are colored according to this structure prediction. In agreement with the prediction, about half of the amide peaks, originating from the structured segment, are widely dispersed (green labels) and have uniform peak intensities while the other half are clustered in a narrow region of the 1HN axis and show great variance in peak intensities, ranging from very weak (e.g. V469–L471 and G491–S495) to very high (e.g. D476–L481).
Cross-references: BMRB:27034
Protein: DP01180 (UniProt Q8RY59)
Region: residues 500	to 511
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Triple-resonance NMR spectra showed significant peak-broadening in the N-terminal region of both variants, as also reported in a recent NMR analysis of RCD1-RST468-589 (Tossavainen et al., 2017).
Although sequential assignment was possible in the free state, structure elucidation was impeded by general peak-broadening, particularly in the N-terminal region.
Cross-references: PDB:5OAO
BMRB:27302
Protein: DP01180 (UniProt Q8RY59)
Region: residues 573	to 589
Annotation: self-interaction (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This  suggests  that  the  flanking  regions induce  a  conformational  state  mimicking  the  bound  state.  In  support  of  this,  amide  CSPs  of  RCD1-RST487-589 correlated well with those of DREB2A-bound RCD1-RST499-572, when using unbound RCD1-RST499-572 as reference (Fig. 1D, top, S1A, Pearson’s r = 0.84).
The amide resonances of this variant overlapped with those of RCD1-RST487-589 confirming the C-terminal tail as the source of the induced changes (Fig. 1C).
Cross-references: BMRB:50545
Protein: DP01181 (UniProt P56621)
Region: residues 2	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystall structure of CnrH ( residues 5–91 and 123–189) and CnrYc (residues 2–30) has been solved.
Cross-references: PDB:4CXF
Protein: DP01181 (UniProt P56621)
Region: residues 2	to 30
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CnrH inhibition by CnrYc.
"CnrYc stabilizes a conformation of CnrH that cannot bind the promoter − 10 element and it occludes the RP core-binding determinants on σ2 and σ4."
Protein: DP01181 (UniProt P56621)
Region: residues 2	to 30
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"The final 1.75-Å-resolution model consists of residues 5–91 and 123–189 of CnrH, and in residues 2–30 of CnrY"
Protein: DP01182 (UniProt P22216)
Region: residues 165	to 190
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density is not discernible for part of the SCD1 domain (residues
1−14), part of the loops of the FHA1 domain (residues 79−86 and 135−137), the linker region between the FHA1 and kinase domains (residues 165−190), part of the activation segment (residues 344−356)
Protein: DP01182 (UniProt P22216)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density is not discernible for part of the SCD1 domain (residues
1−14), part of the loops of the FHA1 domain (residues 79−86 and 135−137), the linker region between the FHA1 and kinase domains (residues 165−190), part of the activation segment (residues 344−356)
Protein: DP01182 (UniProt P22216)
Region: residues 170	to 190
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No discernable electron density was observed for a number of loop regions, including the N-terminal 21 residues preceding the kinase domain (170 to 190), residues 207 to 209 of the glycine-rich loop β1–β2 in molecule B (201 to 209 in molecule A), residues 234 to 237 of loop β3–αC (232 to 238 in molecule B), residues 347 to 357 of the activation segment, residues 369 to 381 of loop αEF–αF, residues 472 to 474, and the C-terminal 16 residues (497 to 512).
Cross-references: PDB:4PDP
Protein: DP01182 (UniProt P22216)
Region: residues 344	to 356
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density is not discernible for part of the SCD1 domain (residues
1−14), part of the loops of the FHA1 domain (residues 79−86 and 135−137), the linker region between the FHA1 and kinase domains (residues 165−190), part of the activation segment (residues 344−356)
Protein: DP01182 (UniProt P22216)
Region: residues 347	to 357
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No discernable electron density was observed for a number of loop regions, including the N-terminal 21 residues preceding the kinase domain (170 to 190), residues 207 to 209 of the glycine-rich loop β1–β2 in molecule B (201 to 209 in molecule A), residues 234 to 237 of loop β3–αC (232 to 238 in molecule B), residues 347 to 357 of the activation segment, residues 369 to 381 of loop αEF–αF, residues 472 to 474, and the C-terminal 16 residues (497 to 512).
Cross-references: PDB:4PDP
Protein: DP01182 (UniProt P22216)
Region: residues 352	to 357
Annotation: phosphorylation display site (Disorder function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
 Phosphorylation was assessed by immunoblot using a Thr354 phospho-specific antibody (α-Rad53pT354).
Protein: DP01182 (UniProt P22216)
Region: residues 368	to 382
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No discernable electron density was observed for a number of loop regions, including the N-terminal 21 residues preceding the kinase domain (170 to 190), residues 207 to 209 of the glycine-rich loop β1–β2 in molecule B (201 to 209 in molecule A), residues 234 to 237 of loop β3–αC (232 to 238 in molecule B), residues 347 to 357 of the activation segment, residues 369 to 381 of loop αEF–αF, residues 472 to 474, and the C-terminal 16 residues (497 to 512)
Cross-references: PDB:4PDP
Protein: DP01182 (UniProt P22216)
Region: residues 497	to 512
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No discernable electron density was observed for a number of loop regions, including the N-terminal 21 residues preceding the kinase domain (170 to 190), residues 207 to 209 of the glycine-rich loop β1–β2 in molecule B (201 to 209 in molecule A), residues 234 to 237 of loop β3–αC (232 to 238 in molecule B), residues 347 to 357 of the activation segment, residues 369 to 381 of loop αEF–αF, residues 472 to 474, and the C-terminal 16 residues (497 to 512).
Cross-references: PDB:4PDP
Protein: DP01183 (UniProt Q9R224)
Region: residues 1	to 128
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As shown in Fig. 6B, the CD spectrum of Bex1 in solution revealed a high level of disorder, although the observed spectrum did not exhibit a completely random coil conformation.
Protein: DP01184 (UniProt O96013)
Region: residues 9	to 68
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Furthermore, it is also lacking of any tight
tertiary packing as evident from its HSQC spectrum which has
narrow spectral dispersions on both 1H and 15N dimensions
Protein: DP01184 (UniProt O96013)
Region: residues 9	to 68
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the present study, we first experimentally demonstrate that
the N-terminal regulatory domain sufficient for auto-inhibiting
PAK4 and binding Cdc42 isintrinsically unstructured.
Protein: DP01184 (UniProt O96013)
Region: residues 9	to 68
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As judged from its far-UV spectrum with the maximal negative
signal at 201 nm (Fig. 1B), the domain is predominantly
unstructured in the free state, without any stable secondary
structures
Protein: DP01185 (UniProt P46669)
Region: residues 95	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The A43 tip loop is flexible in the crystal structure (Figures 3B and S4), but is likely folded upon binding to the Pol I core.
Protein: DP01186 (UniProt P03086)
Region: residues 14	to 23
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we report the resolution of the 3D structure of full-length JCV agnoprotein by NMR, which not only confirmed the existence of the previously reported major α-helix domain at the same position but also revealed the presence of an additional minor α-helix region spanning amino acid residues Leu6 to Ala10. The remaining regions of the protein adopt an intrinsically unstructured conformation.
Average structure of agnoprotein contains two α-helical structures Leu6- Lsy13 and Arg24-Phe39 (colored green) and two principal unstructured regions spanning residues Val14-Lys23 and Cys40-Thr71 (colored red).
Cross-references: PDB:5NHQ
Protein: DP01186 (UniProt P03086)
Region: residues 40	to 71
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we report the resolution of the 3D structure of full-length JCV agnoprotein by NMR, which not only confirmed the existence of the previously reported major α-helix domain at the same position but also revealed the presence of an additional minor α-helix region spanning amino acid residues Leu6 to Ala10. The remaining regions of the protein adopt an intrinsically unstructured conformation.
Average structure of agnoprotein contains two α-helical structures Leu6- Lsy13 and Arg24-Phe39 (colored green) and two principal unstructured regions spanning residues Val14-Lys23 and Cys40-Thr71 (colored red).
Cross-references: PDB:5NHQ
Protein: DP01186 (UniProt P03086)
Region: residues 19	to 23
Annotation: phosphorylation display site (Disorder function)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
Agnoprotein contains several potential phosphorylation sites, including Ser7, Ser11, and Thr21, which are potential targets for the serine/threonine-specific protein kinase C (PKC). In this study, we investigated the functional significance of these phosphorylation sites for the activity of agnoprotein. In vitro and in vivo kinase assays demonstrated that agnoprotein is a target for phosphorylation by PKC. In addition, each of the PKC phosphorylation sites was mutated to Ala singly and in combination, and the effects of these mutations on the JCV life cycle were analyzed.
Evidence corresponding to Thr21.
Protein: DP01186 (UniProt P03086)
Region: residues 19	to 23
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Agnoprotein phosphorylation mutants were unable to sustain infection cycle.
As shown in Fig. ​Fig.3A,3A, as expected, WT virus replicated efficiently during the infection cycle, and its level of replication increased gradually but significantly toward 21 day posttransfection (lanes 2 to 4). However, it was surprising that all three phosphorylation mutants of agnoprotein showed replication only during the early phases of infection cycle (lanes 5, 8, and 11) and were unable to sustain replication cycles at later time points. It was also evident from our results that mutation at Thr21 alone or those at Ser7 and Ser11 were sufficient to cause this effect.
In the present study, we investigated the functional importance of phosphorylation sites of agnoprotein (Ser7, Ser11, and Thr21) by genetic and biochemical approaches and demonstrated that the phosphorylation of respective target sites on agnoprotein by PKC (Ser7, Ser11, and Thr21) is critical for virus propagation.
In conclusion, we have demonstrated that agnoprotein is phosphorylated by PKC and viruses containing phosphorylation mutants of agnoprotein do not propagate after the first round of the infection cycle.
Evidence corresponding to Thr21.
Protein: DP01187 (UniProt P34087)
Region: residues 57	to 68
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered in the Rpb4/7 structure are the Rpb7 tip loop (residues 57– 68)
Protein: DP01187 (UniProt P34087)
Region: residues 57	to 68
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Rpb7 tip domain binds to the Pol II core with the helical turn K1 and with the highly conserved “tip loop,” which is disordered in the free Rpb4/7 structure but folds upon core binding.