LiteFold/DisProt huggingface dataset:
Protein: DP01391 (UniProt P03520)
Region: residues 6	to 33
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Replication of non-segmented negative-strand RNA viruses requires the continuous supply of the nucleoprotein (N) in the form of a complex with the phosphoprotein (P). Here, we present the structural characterization of a soluble, heterodimeric complex between a variant of vesicular stomatitis virus N lacking its 21 N-terminal residues (NΔ21) and a peptide of 60 amino acids (P60) encompassing the molecular recognition element (MoRE) of P that binds RNA-free N (N0). The complex crystallized in a decameric circular form, which was solved at 3.0 Å resolution, reveals how the MoRE folds upon binding to N and competes with RNA binding and N polymerization.
The authors describe a structure of the vesicular stomatitis virus N⁰-P complex (PDB:3PMK), using a recombinant phosphoprotein (UniProt ACC: B7UCZ3) whose N-terminal region is identical to the phosphoprotein here annotated.
Cross-references: PDB:3PMK
Protein: DP01391 (UniProt P03520)
Region: residues 6	to 33
Annotation: viral genome replication (Biological process)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Replication of non-segmented negative-strand RNA viruses requires the continuous supply of the nucleoprotein (N) in the form of a complex with the phosphoprotein (P). Here, we present the structural characterization of a soluble, heterodimeric complex between a variant of vesicular stomatitis virus N lacking its 21 N-terminal residues (NΔ21) and a peptide of 60 amino acids (P60) encompassing the molecular recognition element (MoRE) of P that binds RNA-free N (N0). The complex crystallized in a decameric circular form, which was solved at 3.0 Å resolution, reveals how the MoRE folds upon binding to N and competes with RNA binding and N polymerization.
The authors describe a structure of the vesicular stomatitis virus N⁰-P complex (PDB:3PMK), using a recombinant phosphoprotein (UniProt ACC: B7UCZ3) whose N-terminal region is identical to the phosphoprotein here annotated.
Protein: DP01391 (UniProt P03520)
Region: residues 1	to 60
Annotation: RNA folding chaperone (Molecular function)
Evidence: static light scattering assay evidence used in manual assertion
Supporting statements:
The characterization by absorbance spectroscopy and size-exclusion chromatography (SEC) combined with static light scattering (MALLS) demonstrates that both NΔ210-P60 and NΔ210-P dimer complexes are free of RNA in solution, forming soluble heterodimers or heterotrimers, respectively. Therefore, P60 fulfills both chaperone activities of full-length P.
The authors use a recombinant phosphoprotein (UniProt ACC: B7UCZ3) whose N-terminal region (1-60) is identical to the phosphoprotein here annotated.
Protein: DP01392 (UniProt P53330)
Region: residues 35	to 53
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density.
Cross-references: PDB:4I6M
Protein: DP01392 (UniProt P53330)
Region: residues 36	to 53
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:5TGC
Protein: DP01392 (UniProt P53330)
Region: residues 91	to 157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:5TGC
Protein: DP01392 (UniProt P53330)
Region: residues 91	to 157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density.
Cross-references: PDB:4I6M
Protein: DP01396 (UniProt P01130)
Region: residues 163	to 175
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 12 residue linker connecting the modules, though slightly structured through an interaction with LA4, is highly flexible.
Cross-references: PDB:2LGP
Protein: DP01396 (UniProt P01130)
Region: residues 163	to 175
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Across species, evolution has conserved the length (12–14 residues) of the linker between LA4 and LA5 without conservation of any specific residues, which is typically seen for flexible linkers.
Protein: DP01396 (UniProt P01130)
Region: residues 163	to 175
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Truncation of this linker significantly alters the interaction with LDL particles hinting that it may be required for the two modules to access distant epitopes on ligands such as multiple copies of ApoE on a lipoprotein surface.
Protein: DP01396 (UniProt P01130)
Region: residues 354	to 393
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No interpretable electron density was observed for the EGF(B) domain, suggesting that it is disordered in the crystals
Cross-references: PDB:2W2Q
PDB:2W2P
PDB:2W2O
PDB:2W2N
PDB:2W2M
Protein: DP01397 (UniProt Q9Z0P7)
Region: residues 279	to 359
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
3.2. SUFU contains an intrinsically disordered region
Protein: DP01398 (UniProt G0SCY6)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Only small parts of the structure are disordered. HypK: residues 1–25, 43–56
Cross-references: PDB:5NNR
Protein: DP01398 (UniProt G0SCY6)
Region: residues 1	to 25
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Our study also shows that the regulatory function of HypK resides in its N-terminal region comprising the first 50 residues (disordered N terminus and helix α1), which bind at the entrance of the Naa10 active site and seem to block access to the active site.
Protein: DP01399 (UniProt G0S4M4)
Region: residues 573	to 637
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Small parts of the structure are disordered: the lysine-rich region (charged helix) 573–637.
Cross-references: PDB:5NNP
Protein: DP01400 (UniProt P45985)
Region: residues 49	to 62
Annotation: mitogen-activated protein kinase p38 binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Large increases in the 15N R2 rates are observed even for small molar ratios of p38α for all residues of the docking site motif and the KIS domain, as well as for residues immediately adjacent to these regions. These results confirm the extended nature of the MKK4 interaction site with p38α.
Cross-references: ELM:DOC_MAPK_MEF2A_6
Protein: DP01400 (UniProt P45985)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary 13Cα chemical shifts show that this domain is devoid of transiently populated secondary structures (Figure 2C). Nuclear relaxation rates can be used to probe the dynamics of IDPs on the pico- to nanosecond time scale including correlated motions.
Protein: DP01400 (UniProt P45985)
Region: residues 12	to 86
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Line broadening is observed for multiple residues upon addition of JNK1 demonstrating a clear interaction, while chemical shift changes are negligible (Figure 1). We quantified the intensities of the resonances as a function of the molar ratio of JNK1 showing that the interacting region extends over a large part of the MKK4 sequence with the docking site motif (40KRKALKLNF48) experiencing the most pronounced line broadening (Figure 2).
Protein: DP01400 (UniProt P45985)
Region: residues 12	to 86
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We compared the thermodynamic profiles of the MKK4:JNK1 and MKK4:p38α complexes by using ITC (Figure 4). Both complexes show a 1:1 stoichiometry with the JNK1 complex displaying an approximately three times higher binding affinity (KD = 1.3 μM) than the p38α complex (KD = 4.1 μM).
This entry corresponds to the experimental evidences of two independent heterodimers MKK4:JNK1 and MKK4:p38α. Binding free energies reveal that JNK1 and p38α binding to MKK4 are governed by different thermodynamic contributions. p38α ruled by a clear entropic contribution, while the enthalpy compensates the lack of entropic contribution for the JNK1 interaction.
Protein: DP01400 (UniProt P45985)
Region: residues 38	to 49
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The results show that MKK4 folds into two different conformations upon binding to JNK1 and p38α. While MKK4 shows poor helical propensity in complex with p38α, it folds into a helix encompassing residues K40-K45 upon binding to JNK1 (Figure 6a). We note that a conformational selection mechanism can be ruled out in the case of the JNK1 complex, as MKK4 does not show any helical propensity in its free state (Figure 6a) [35]. 
Despite prominent helix is comprised between residues 40 and 45, the region between residue 28 and 49 shows significant population of α-helix as calculated from the experimental chemical shifts.
Protein: DP01400 (UniProt P45985)
Region: residues 41	to 48
Annotation: mitogen-activated protein kinase p38 binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Addition of the canonical docking site peptide of MKK4 (residues 39–50) leads to CSPs primarily in three different regions of p38α involving residues 110–129, 160–164, and 304–320 that are all located at or in close proximity to the docking groove.
Cross-references: ELM:DOC_MAPK_MEF2A_6
Protein: DP01400 (UniProt P45985)
Region: residues 40	to 48
Annotation: mitogen-activated protein kinase binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We quantified the intensities of the resonances as a function of the molar ratio of JNK1 showing that the interacting region extends over a large part of the MKK4 sequence with the docking site motif (40KRKALKLNF48) experiencing the most pronounced line broadening (Figure 2).
Cross-references: ELM:DOC_MAPK_NFAT4_5
Protein: DP01401 (UniProt P47093)
Region: residues 68	to 109
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both the RNA-free and RNA-bound Lsm complexes, the following regions have no clear electron density and are absent in the final atomic models: residues 90–95 of Lsm2, residues 80–89 of Lsm3, residues 87–93 of Lsm4, residues 1–5 and 85–93 of Lsm5, residues 1–10 of Lsm6, residues 1–26 and 106–115 of Lsm7, residues 68–109 of Lsm8. These sequences are all located on the surface and presumably highly flexible.
Cross-references: PDB:4M7A
PDB:4M7D
PDB:4M78
PDB:4M77
Protein: DP01402 (UniProt Q06406)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For both the RNA-free and RNA-bound Lsm complexes, the following regions have no clear electron density and are absent in the final atomic models: residues 90–95 of Lsm2, residues 80–89 of Lsm3, residues 87–93 of Lsm4, residues 1–5 and 85–93 of Lsm5, residues 1–10 of Lsm6, residues 1–26 and 106–115 of Lsm7, residues 68–109 of Lsm8. These sequences are all located on the surface and presumably highly flexible.
Cross-references: PDB:4M7A
PDB:4M7D
PDB:4M75
PDB:4M78
PDB:4M77
Protein: DP01404 (UniProt Q92913)
Region: residues 213	to 237
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
After completion of diffraction data collection, the crystal was analyzed by mass spectrometry, which indicated that FHF2A residues 60–237 are within the boundaries of the crystallized FHF2A protein.
The final model for the FHF2A structure contains residues 64–212 of two FHF2A molecules; residues 60–63 at the N terminus and 213–237 at the C terminus are disordered in each of the two molecules.
Cross-references: PDB:3HBW
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We calculated secondary structure propensities (SSPs) based on experimental Cα and Cβ chemical shifts, which indicate that no strong propensities for either α-helical or extended structure exist (Fig. 2a).
 The obtained conformational ensembles describe B/NPTAIL as a protein behaving much like a statistical coil, with the exception of a region starting around residue 59 that had a slightly increased propensity to form right handed α-helices as compared to random coil.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: importin-alpha family protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, the interaction between B/NPTAIL and importin-α involves all residues of the disordered tail between amino acids 30 and 71 (Fig. 4c).
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The experimental SAXS curve of full length B/NP was in reasonable agreement (chi2 below 1) with this conformational ensemble (Fig. 2d).
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: importin-alpha family protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
An absence of linearity in the Guinier plot reflects the presence of aggregates and/or attractive/repulsive interactions between the scattering particles.
The complex between importin-α7 and B/NP was studied with SAXS. The analysis shows the volumes of the two proteins. Although the SAXS envelope of a disordered chain cannot give a single structure for B/NTAIL the complex shows that importin-α binds two thirds of the tail, concordant with the results from NMR, and no other parts of B/NP.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: importin-alpha family protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The peak eluted at 12.5 mL corresponds to the B/NPTAIL and the SDS-PAGE gel confirms the presence of the protein contained in that elution peak (band at 15 kDa). The elution peak at 10.5 mL corresponds to importin-α7 alone and the peak at 10.1 mL corresponds to the complex between B/NPTAIL and importin-α7. These results confirm that importin-α7 binds the full-length influenza B nucleoprotein and its N-terminal tail but not B/NPCORE.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: importin-alpha family protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
B/NPTAIL binds human importin-α7 with a K d of 844 nM, similar to the affinity measured between A/NP and the mouse importin-α1 (K d between 2 and 5 µM)19,20.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: NLS-bearing protein import into nucleus (Biological process)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The peak eluted at 12.5 mL corresponds to the B/NPTAIL and the SDS-PAGE gel confirms the presence of the protein contained in that elution peak (band at 15 kDa). The elution peak at 10.5 mL corresponds to importin-α7 alone and the peak at 10.1 mL corresponds to the complex between B/NPTAIL and importin-α7. These results confirm that importin-α7 binds the full-length influenza B nucleoprotein and its N-terminal tail but not B/NPCORE.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: NLS-bearing protein import into nucleus (Biological process)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The complex between importin-α7 and B/NP was studied with SAXS. The analysis shows the volumes of the two proteins. Although the SAXS envelope of a disordered chain cannot give a single structure for B/NTAIL the complex shows that importin-α binds two thirds of the tail, concordant with the results from NMR, and no other parts of B/NP.
Protein: DP01405 (UniProt Q5V913)
Region: residues 1	to 70
Annotation: NLS-bearing protein import into nucleus (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, the interaction between B/NPTAIL and importin-α involves all residues of the disordered tail between amino acids 30 and 71 (Fig. 4c).
Protein: DP01407 (UniProt O61667)
Region: residues 93	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 2 residues and the C-terminal 14 residues in EGL-1 have no electron density in the maps, and we presume that these regions are disordered in the crystals.
Cross-references: PDB:1TY4
Protein: DP01420 (UniProt Q16543)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
N-Cdc37 secondary structure: straight and zigzag lines illustrate unstructured and helical regions, respectively.
In summary, N-Cdc37 forms an independently folded domain that adopts a two-helix bundle conformation and displays differential dynamics containing long N- and C-terminal flexible tails.
Cross-references: PDB:2NCA
Protein: DP01420 (UniProt Q16543)
Region: residues 112	to 126
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
N-Cdc37 secondary structure: straight and zigzag lines illustrate unstructured and helical regions, respectively.
In summary, N-Cdc37 forms an independently folded domain that adopts a two-helix bundle conformation and displays differential dynamics containing long N- and C-terminal flexible tails
Cross-references: PDB:2NCA
Protein: DP01420 (UniProt Q16543)
Region: residues 344	to 378
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
On the other hand, residues in the segment 345–378 exhibit low (<0.3) or even negative values suggesting that this is an inherently flexible region, where ps–ns dynamics are operative and ample backbone conformational heterogeneity is present
In contrast, for the 35 C-terminal residues that are predicted disordered and have low {1H}–15N NOEs, this drops to 2.9 s−1.
Cross-references: PDB:2N5X
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 111
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions.
The lack of dispersion in the backbone amide 1H chemical shifts as seen in the 1H-15N HSQC spectrum gives evidence of the largely disordered and flexible nature of p15PAF under native conditions.
1H-15N RDCs of p15PAF measured in a stretched polyacrylamide gel aligning medium are mainly negative (Fig. 4, black circles), as observed in disordered proteins (16,47).
Cross-references: BMRB:19332
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 111
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions.
The far-UV CD spectrum of p15PAF shows a minimum at 198 nm and a shoulder at 222 nm, consistent with a predominantly random-coil protein with little secondary structure (Fig. 2 B). The thermal denaturation curve of p15PAF followed by the changes in the CD signal at 222 nm (see Fig. 2 B, inset) does not show any cooperative folding-unfolding transition, indicating that p15PAF lacks a defined tertiary structure.
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 111
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions.
We used SAXS to characterize the conformational space sampled by p15PAF in solution and to validate the structure ensemble derived from the RDC data. As shown in Fig. 5, the SAXS profile of p15PAF and its Kratky representation are typical for a disordered protein. The SAXS curve shows no features (Fig. 5 A) and the Kratky plot does not show a maximum, with a monotonic increase at large momentum transfer values (Fig. 5 B).
Protein: DP01425 (UniProt Q15004)
Region: residues 1	to 111
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions.
The protein eluted from the SEC column at a volume that, according to the calibration with molecular weight standards, corresponds to an apparent molar mass of 25 kDa. However, the mass derived from the MALLS data is 11.5 kDa (Fig. 2 A), demonstrating that p15PAF is monomeric. These inconsistent results suggest that p15PAF is either folded with an elongated shape or is flexible and disordered (39). In both instances, it would elute at a smaller volume than a globular protein of the same mass.