LiteFold/DisProt huggingface dataset:
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1444	to 1455
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues V76-V87 of NS2B which form a β-hairpin in the crystal structure, are relatively flexible in solution and exhibit relatively broaden peaks, suggesting a dynamic sampling process of the NS2B cofactor binding to NS3 and forming the P2 pocket (Fig. 1b; Supplementary Fig. 6).
Cross-references: PDB:5GJ4
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1444	to 1455
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues V76-V87 of NS2B which form a β-hairpin in the crystal structure, are relatively flexible in solution and exhibit relatively broaden peaks, suggesting a dynamic sampling process of the NS2B cofactor binding to NS3 and forming the P2 pocket (Fig. 1b; Supplementary Fig. 6).
Cross-references: PDB:5GJ4
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1499	to 1512
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The PDB corresponds to the Uniprot A0A140DLX4 and shows disorder in the region 1503-1516. IDR is 100% identical to this Uniprot and comprises the residues 1499-1512.
Cross-references: PDB:5GJ4
DisProt:DP03524
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2822	to 2836
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 15 N-terminal and last 16 C-terminal residues are not visible in the electron density. Due to disorder, parts of loops 1 (residues 340–363), 3 (residues 408–417), 4 (residues 454–471), 5 (residues 533–542) and 6 (residues 576–606) are also missing in the model.
The 15 N-terminal region of the Zika virus RNA-dependent RNA polymerase corresponds to the 2822-2836 region of the polyprotein.
Cross-references: PDB:5U04
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2857	to 2879
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 15 N-terminal and last 16 C-terminal residues are not visible in the electron density. Due to disorder, parts of loops 1 (residues 340–363), 3 (residues 408–417), 4 (residues 454–471), 5 (residues 533–542) and 6 (residues 576–606) are also missing in the model.
The 340-363 region of the Zika virus RNA-dependent RNA polymerase corresponds to the 2857-2879 region of the polyprotein.
Cross-references: PDB:5U04
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2971	to 2986
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 15 N-terminal and last 16 C-terminal residues are not visible in the electron density. Due to disorder, parts of loops 1 (residues 340–363), 3 (residues 408–417), 4 (residues 454–471), 5 (residues 533–542) and 6 (residues 576–606) are also missing in the model.
The 454-471 region of the Zika virus RNA-dependent RNA polymerase corresponds to the 2971-2986 region of the polyprotein.
Cross-references: PDB:5U04
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 3093	to 3121
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 15 N-terminal and last 16 C-terminal residues are not visible in the electron density. Due to disorder, parts of loops 1 (residues 340–363), 3 (residues 408–417), 4 (residues 454–471), 5 (residues 533–542) and 6 (residues 576–606) are also missing in the model.
The C-terminal region of the Zika virus RNA-dependent RNA polymerase corresponds to the 3404-3419 region of the polyprotein.
Cross-references: PDB:5U04
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2116	to 2163
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of NS4A (1–48) is showing a minimum (negative peak) at 199 nm (Fig. 2), and the ellipticity value beyond 199 nm showing no signature peak that suggests missing helices and beta-strands. Shape of the spectrum and signature minima indicating the Far-UV CD spectrum of typically disordered (unstructured or natively unfolded) protein.
The 1-48 region of the NS4A protein corresponds to the 2116-2163 region of the Zika virus polyprotein.
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2116	to 2163
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of NS4A (1–48) peptide is of disordered type as observed in the previous section, but when this peptide is mixed with lipid vesicles (DOPC or DOPS), it displays spectra of a helix (Fig. 5A and B).
While increasing SDS concentration up to 0.5 mM and beyond, a spectral shift was observed at 199 nm and 222 nm, indicating a transition from disordered to α-helix (Fig. 5D).
The 1-48 region of the NS4A protein corresponds to the 2116-2163 region of the Zika virus polyprotein.
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 2116	to 2163
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of NS4A (1–48) peptide is of disordered type as observed in the previous section, but when this peptide is mixed with lipid vesicles (DOPC or DOPS), it displays spectra of a helix (Fig. 5A and B).
The SDS micelles further probed the structural transition in NS4A (1–48). SDS is an anionic detergent that, upon interaction, causes a conformational change in many proteins (Blinkhorn and Jones, 1973; Moriyama et al., 2008; Singh et al., 2008).
The 1-48 region of the NS4A protein corresponds to the 2116-2163 region of the Zika virus polyprotein.
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1441	to 1468
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
While 15N-labeled ZIKV NS2B in complex with unlabeled ZIKV NS3pro had a narrowly-dispersed HSQC spectrum with only ~29 peaks detectable (S2B Fig), Dengue NS2B in complex with Dengue NS3pro domain has a well-dispersed HSQC spectrum (S2C Fig) [21,30,31] which unambiguously indicates Dengue NS2B has a tight tertiary packing unlike the Zika one.
The NS2B peptide used corresponds to the 1416-1468 residues of the Zika virus genome polyprotein.
Our NMR results here indicated that only C-terminal residues of ZIKV NS2B remained disordered both in the complex form (Arg73-Lys100; Fig 2E) and in presence of BPTI (Leu86-Lys100; Fig 2F), and the conformation of these C-terminal residues in ZIKV NS2B in these two forms are similar to the uncomplexed form as their HSQC peaks are superimposable (Fig 2C).
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1416	to 1468
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The small absolute values of (ΔCα-ΔCβ) chemical shifts over the whole sequence clearly indicate that the isolated Zika NS2B (48–100) lacks stable secondary structure.
The NS2B peptide used corresponds to the 1416-1468 residues of the Zika virus genome polyprotein.
Protein: DP01256 (UniProt Q32ZE1)
Region: residues 1416	to 1440
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The small absolute values of (ΔCα-ΔCβ) chemical shifts over the whole sequence clearly indicate that the isolated Zika NS2B (48–100) lacks stable secondary structure.
The NS2B peptide used corresponds to the 1416-1468 residues of the Zika virus genome polyprotein.
Our NMR results here indicated that only C-terminal residues of ZIKV NS2B remained disordered both in the complex form (Arg73-Lys100; Fig 2E) and in presence of BPTI (Leu86-Lys100; Fig 2F), and the conformation of these C-terminal residues in ZIKV NS2B in these two forms are similar to the uncomplexed form as their HSQC peaks are superimposable (Fig 2C).
Protein: DP01259 (UniProt P41208)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered HsCen-2 N-terminal Residues—One aspect missing from the HsCen-2 structure is the sequence of amino acids numbered 1-22 from the N-terminal domain, which were determined to be disordered.
Protein: DP01261 (UniProt P53905)
Region: residues 1	to 26
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 1–26 and 106–115 of Lsm7. 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: DP01261 (UniProt P53905)
Region: residues 105	to 115
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 1–26 and 106–115 of Lsm7. 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: DP01262 (UniProt P49848)
Region: residues 1	to 216
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We were unable to detect density near either copy of the TAF6C homodimer for the N-terminal histone fold domain of TAF6, which forms a heterodimer with the histone fold domain of TAF915.
Cross-references: PDB:5FUR
Protein: DP01262 (UniProt P49848)
Region: residues 437	to 677
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered in the Cryo-EM structure of the human TFIID-IIA bound to core promoter DNA.
Cross-references: PDB:5FUR
EMDB:3305
Protein: DP01268 (UniProt Q9H816)
Region: residues 314	to 335
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the C-terminal peptide (314–335) is not visible in the structure and is assumed to be disordered.
Cross-references: PDB:5AHO
Protein: DP01269 (UniProt Q8NG31)
Region: residues 176	to 200
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is interpretable electron density for residues 175–189 of Knl1, whereas the rest of the polypeptide chain is presumably disordered in solvent and therefore invisible in the electron density.
Cross-references: PDB:4A1G
Protein: DP01269 (UniProt Q8NG31)
Region: residues 217	to 226
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is interpretable electron density for residues 175–189 of Knl1, whereas the rest of the polypeptide chain is presumably disordered in solvent and therefore invisible in the electron density.
Cross-references: PDB:4A1G
Protein: DP01269 (UniProt Q8NG31)
Region: residues 234	to 252
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Far-UV circular dichroism spectra reveal a predominantly disorder structure of Blinkin peptide S208-K226 in aqueous solutions.
Region 208-226 of the Isoform 2 (identifier: Q8NG31-2), used in this study, corresponds to the 234-252 region of the Isoform 1.
Protein: DP01269 (UniProt Q8NG31)
Region: residues 237	to 251
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
However, the structure reveals that this Blinkin region undergoes a dramatic disorder-to-order transition upon BUBR1 binding, a feature also observed in TFE-titration experiments of Blinkin mimic peptides monitored by circular dichroism (Figure 3C and inset).
Electron density of the Blinkin residues N211-G225 was clearly visible and unequivocally shows that the side chains of Blinkin residues I213, F215, F218, and I219 form part of a short α helix defined by residues F215-T224 (Figure 2D) that runs parallel to the long axis of BUBR1 TPR1 and TPR2.
Region 208-226 of the Isoform 2 (identifier: Q8NG31-2), used in this study, corresponds to the 234-252 region of the Isoform 1. The residues the authors are referring as visible are N237-251.
Cross-references: PDB:3si5
Protein: DP01269 (UniProt Q8NG31)
Region: residues 234	to 252
Annotation: protein binding (Molecular function)
Evidence: electrospray ionization fourier transform ion cyclotron resonance mass spectrometry evidence used in manual assertion
Supporting statements:
Nano-ESI MS of synthetic peptides that mimic Blinkin S208-K226 confirm the interaction while peptides harbouring site-specific substitutions indicate the hydrophobic residues I213, F215, F218 and I219 are critical for binding BUBR1.
Region 208-226 of the Isoform 2 (identifier: Q8NG31-2), used in this study, corresponds to the 234-252 region of the Isoform 1. In this sense, residues critical for the interaction are I239, F241, F244 and I245.
Protein: DP01269 (UniProt Q8NG31)
Region: residues 234	to 252
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The micromolar binding affinity of Blinkin S208-K226 peptide for BUBR157-220 (9.3 μM ± 0.4 in 1:1 stoichiometry) reflects a relatively moderate interaction. Nano-ESI MS and 2D NMR titration data confirmed the 1:1 stoichiometry of the interaction.
Cross-references: BMRB:17960
Protein: DP01269 (UniProt Q8NG31)
Region: residues 234	to 252
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The 2.2 Å Crystal Structure of the BUBR1-Blinkin Complex Reveals an Unexpected Mode of Binding
Cross-references: PDB:3SI5
Protein: DP01271 (UniProt Q15691)
Region: residues 256	to 268
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The carboxy-terminal acidic sequence segment of EB1c is disordered beyond Thr249 in both copies, and the interaction of residues 249–255 with p150n seen in the contact A mode of EB1c-p150n (Figure 2B) is not present.
Cross-references: PDB:2HKQ
Protein: DP01271 (UniProt Q15691)
Region: residues 252	to 268
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In free EB1c, the polypeptide segment 194–250 is predominantly structured in solution, whereas the segment 252–268 appears to be flexibly disordered. In complex with APCp1, residues 250–257 of EB1c become ordered (Figure 6B), and chemical shift changes indicate that these residues together with residues 213–225 and 247–249 of the hydrophobic cavity and the polar rim are the major interaction sites (Figure 6C; Figure S7).
Protein: DP01271 (UniProt Q15691)
Region: residues 250	to 257
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In free EB1c, the polypeptide segment 194–250 is predominantly structured in solution, whereas the segment 252–268 appears to be flexibly disordered. In complex with APCp1, residues 250–257 of EB1c become ordered (Figure 6B), and chemical shift changes indicate that these residues together with residues 213–225 and 247–249 of the hydrophobic cavity and the polar rim are the major interaction sites (Figure 6C; Figure S7).
Protein: DP01272 (UniProt Q03132)
Region: residues 908	to 922
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
no electron density was observed for two N-terminal residues, fourteen C-terminal residues, and eleven residues from two internal disordered regions.
Cross-references: PDB:2QO3
Protein: DP01272 (UniProt Q03132)
Region: residues 2641	to 2653
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three regions of the constructed DH fragment were unobservable in the electron density maps: 1) the N-terminal histidine tag and H2362-A2365, (2) the C-terminal residues S2641-G2653, and 3) the loop P2582-G2585.
Cross-references: PDB:3EL6
Protein: DP01277 (UniProt Q6VMQ6)
Region: residues 938	to 964
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered 32 N-terminal (five amino acids (GSPEF) from the vector and residues 938 –964 of
MCAF1), the 6 C-terminal residues of SIM MCAF1 , and the 15 N-terminal residues of SUMO-3 are omitted from all
figures for clarity
Protein: DP01278 (UniProt Q68DK7)
Region: residues 558	to 568
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered regions in MSL1 and MSL3 are shown as dots.
Protein: DP01279 (UniProt Q8N5Y2)
Region: residues 226	to 246
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered regions in MSL1 and MSL3 are shown as dots.
Cross-references: PDB:2Y0N
Protein: DP01279 (UniProt Q8N5Y2)
Region: residues 508	to 518
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered regions in MSL1 and MSL3 are shown as dots.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the unoxidized Aβ(1−40) initially produces a CD spectrum characteristic of a random coil, but this changes over several days (Figure 1b) to that of a β-sheet structure that is associated with aggregation and fibril formation.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the unoxidized Aβ(1−40) initially produces a CD spectrum characteristic of a random coil, but this changes over several days (Figure 1b) to that of a β-sheet structure that is associated with aggregation and fibril formation.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the unoxidized Aβ(1−40) initially produces a CD spectrum characteristic of a random coil, but this changes over several days (Figure 1b) to that of a β-sheet structure that is associated with aggregation and fibril formation.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 686
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The main structural feature is an α-helix spanning residues 16−24. The rest of the peptide appears to be disordered with poor superimposition in other regions, including the second helical region (residues 28−36, rmsd of 2.2 Å) found for Aβ(1−40).
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A noticeably different CD spectrum is apparent in the filtrate, which shows a strong minimum near 198 nm indicative of a predominantly disordered structure (Fig. 1a, blue) very similar to that of early aggregation states of Aβ (Fig. 1a, red).
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, this finding suggests a dynamic and disordered structure with a high degree of turns and twists but without a well-defined secondary structure.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: amyloid fibril formation (Biological process)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
Conversely, an intense ThT signal is present in the isolated fibril fraction. Measuring the concentration of the spin-X filtrate by the bicinchoninic acid (BCA) protein concentration assay (Thermo Scientific) revealed 17.0 ± 6.0 μM or only 7.3 + 2.6% of the total Aβ1-40 concentration (231 μM) was not fibrillar. Together, the ThT, CD, and BCA results confirm the sample primarily consists of amyloid fibrils with a minority population of a largely disordered, relatively low MW species.
Protein: DP01280 (UniProt P05067)
Region: residues 672	to 711
Annotation: amyloid fibril formation (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast to the sparse spectra obtained from unaggregated Aβ1-40, the RFDR-based 2D 1H/1H spectra of the aggregated sample showed multiple cross-peaks consistent with the presence of the disordered oligomer suggested by the CD, fluorescence, and AFM experiments (Fig.1).
Protein: DP01281 (UniProt Q9JM54)
Region: residues 16	to 42
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
NoxaA, Puma, NoxaB and
Bim BH3 domains have CD spectra typical for unstructured
peptides
Protein: DP01281 (UniProt Q9JM54)
Region: residues 16	to 42
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Although in isolation the Puma and NoxaA BH3
peptides are unstructured in solution, when bound
to Mcl-1, they form well-ordered α-helices
Cross-references: PDB:2ROD
Protein: DP01281 (UniProt Q9JM54)
Region: residues 16	to 42
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Although in isolation the Puma and NoxaA BH3
peptides are unstructured in solution, when bound
to Mcl-1, they form well-ordered α-helices
Protein: DP01281 (UniProt Q9JM54)
Region: residues 73	to 93
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
NoxaA, Puma, NoxaB and
Bim BH3 domains have CD spectra typical for unstructured
peptides