LiteFold/DisProt huggingface dataset:
Protein: DP03519 (UniProt P27284)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The capsid N-terminal domain (NTD) is disordered and binds the negatively charged alphavirus RNA genome (Owen and Kuhn, 1996).
Despite the identification of the NTD genome-binding sequence on the capsid protein more than 20 years ago (Owen and Kuhn, 1996), the structure of this domain has remained elusive, probably because the capsid NTD sequence (Met1-Ile116 in EEEV) shows features characteristic of intrinsically disordered proteins (Uversky, 2013) with high concentrations of basic residues Arg and Lys (27% of the sequence) and structure-disrupting Pro and Gly residues (26% of the sequence).
Cross-references: PDB:6MX7
Protein: DP03520 (UniProt P15183)
Region: residues 1	to 59
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Each capsid protein is comprised of three domains: the first ~60 residues at the N-terminal region (R), the shell (S) domain, and the protruding (P) domain (Fig. 2A). The first ~90 residues are disordered in the A and B subunits, while the first ~60 residues are disordered in the C subunit.
Cross-references: PDB:4LLF
Protein: DP03521 (UniProt Q58MU6)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all three structures, the N-terminal 20 residues were found to be disordered.
In the final model, the first 20 residues (18 in the case of chain A) have been omitted due to missing density.
Cross-references: PDB:2VCL
Protein: DP03522 (UniProt Q9QR71)
Region: residues 1077	to 1129
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1077-1129 region.
Cross-references: DisProt:DP02334r001
Protein: DP03522 (UniProt Q9QR71)
Region: residues 1098	to 1116
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1098-1116 region.
Cross-references: DisProt:DP02334r003
BMRB:26042
PDB:2ND0
Protein: DP03522 (UniProt Q9QR71)
Region: residues 1098	to 1116
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1098-1116 region.
Cross-references: DisProt:DP02334r004
BMRB:26042
PDB:2ND0
Protein: DP03522 (UniProt Q9QR71)
Region: residues 1098	to 1116
Annotation: viral life cycle (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The LANA gene fragment used in this publication was derived from the Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). IDR is 100% identical and corresponds to 1098-1116 region.
Cross-references: DisProt:DP02334r015
BMRB:26042
PDB:2ND0
Protein: DP03523 (UniProt C4LQ26)
Region: residues 127	to 146
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Only aa 125, 126, and 147 to 149 were visible in the density map, showing that this loop is highly flexible.
Cross-references: PDB:3TJ0
Protein: DP03523 (UniProt C4LQ26)
Region: residues 1	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron densities for the first 71 residues of BNP were not visible, indicating that this N-terminal region of the protein is highly flexible.
Cross-references: PDB:3TJ0
Protein: DP03523 (UniProt C4LQ26)
Region: residues 1	to 70
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron densities for the first 71 residues of BNP were not visible, indicating that this N-terminal region of the protein is highly flexible.
Cross-references: PDB:3TJ0
Protein: DP03523 (UniProt C4LQ26)
Region: residues 127	to 146
Annotation: RNA binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Deletion of this loop in BNP resulted in a 14-fold decrease in the RNA-binding affinity, which is significantly more dramatic than the 6.4-fold decrease in the flexible loop-deleted ANP equivalent (21), implying that this loop in BNP contributes more to RNA binding.
Protein: DP03523 (UniProt C4LQ26)
Region: residues 127	to 146
Annotation: viral life cycle (Biological process)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Deletion of this loop in BNP resulted in a 14-fold decrease in the RNA-binding affinity, which is significantly more dramatic than the 6.4-fold decrease in the flexible loop-deleted ANP equivalent (21), implying that this loop in BNP contributes more to RNA binding.
Protein: DP03524 (UniProt A0A140DLX4)
Region: residues 1503	to 1516
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows disorder in the region 1503-1516. 
Cross-references: PDB:5LC0
Protein: DP03524 (UniProt A0A140DLX4)
Region: residues 1421	to 1466
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We have taken the longest MoRF region of NS2B for this aim. Amino acid sequence of synthesized peptide of NS2B protein residues 49–95 from NS2B–NS3 protease (PDB ID 5LC0 [44]) is [NH2]VDMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEDDGPPMA[COOH]. This synthesized peptide contains our region of interest that is MoRF region (56–78) of the sequence [NH2]AGDITWEKDAEVTGNSPRLDVAL[COOH].
Figure 8 represents the observed far-UV CD spectrum of this peptide and shows that it corresponds to the CD spectrum of a highly disordered, random coil-like polypeptide. This is evidenced by an intensive minimum in the vicinity of 200 nm and the absence of a strong negative signal above 210 nm, which is characteristic of α-helix or β-sheet secondary structure. Therefore, the far-UV CD spectrum of this synthesized NS2B peptide shown in Fig. 8 illustrates the absence of ordered secondary structure, confirming its IDPR nature.
Protein: DP03525 (UniProt Q8JUX6)
Region: residues 1728	to 1744
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A, Ensemble of 20 lowest-energy structures. Disordered residues Ser-1728–The-1729, Gly-1740–Thr-1744 of CHIKV, and the side chain of Arg-1738 have been left out for clarity.
The partially disordered state of nsP3 arginines offers a large binding epitope while minimizing entropic penalty upon binding to amp-SH3.
Cross-references: PDB:5I22
Protein: DP03525 (UniProt Q8JUX6)
Region: residues 1728	to 1744
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Further analysis of CHIKV nsP3 binding using ITC (Table 1 and Fig. 3B) showed that the affinity of this viral peptide to amp-SH3 is unusually high, with a Kd of 0.024 μm, clearly among the strongest found for SH3 domains (18).
The partially disordered state of nsP3 arginines offers a large binding epitope while minimizing entropic penalty upon binding to amp-SH3.
Cross-references: PDB:5I22
Protein: DP03526 (UniProt P12504)
Region: residues 157	to 176
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Clear electron density was observed in the 2Fo-Fc map for Vif residues 140 to 155 before their inclusion in the model. These residues correspond to the Vif BC-box helix that includes the consensus sequence of SLQYLA. The C terminus of the Vif construct, containing the Cullin box, was disordered and not observed in the crystal structure.
According to the PDB 157-176 are the correct boundaries for the disordered region.
Cross-references: PDB:3DCG
Protein: DP03526 (UniProt P12504)
Region: residues 155	to 172
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The fact that the T1 values of BC-box are consistently the same over the span of residues 144–154 indicates that this region is less dynamic and tumbles isotropically compared with the rest residues of the SOCS-box. However, it is of note that the N-terminal-fused tag attached to this region may also contribute to its limited motion.
Cross-references: BMRB:19333
PDB:2MA9
Protein: DP03527 (UniProt D2CPS8)
Region: residues 1	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The dispersion of the resonances in 15N-1 H HSQC spectra of Tat1–72 (Fig. (7)) is typical for disordered proteins lacking regular secondary structure and agrees with previous homonuclear NMR studies [119,120,129,140,141].
Protein: DP03527 (UniProt D2CPS8)
Region: residues 1	to 72
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The strong negative ellipticity at 198 nm shown in Fig. (4) is characteristic of a backbone dominated by the random coil conformation.
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
To obtain residue-specific information regarding the Rev ARM peptide, we recorded 1HN,15N-HSQC spectra (Fig. 2). In aqueous solution, the peptide shows little dispersion of the resonances (Fig. 2 B), indicative of an unfolded peptide and in accordance with the CD data.
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra of the Rev ARM peptide in physiological buffer exhibited a minimum around 200 nm, typical of an unfolded state (Fig. 1 A).
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 5 B shows that the [1HN],15N hetNOE values for Rev ARM in aqueous solution at pH 7.4 average 0.47 for residues T34–R50, consistent with a disordered peptide. In contrast, the hetNOEs of the Rev ARM peptide in complex with RRE StemIIB average 0.83 for residues T34–R50, and in 50% TFE average 0.77 for residues T34–R50. These higher hetNOE values indicate higher backbone rigidity and are typical of a well-ordered secondary structure.
RRE StemIIB it's the RNA binding Rev ARM.
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 5 B shows that the [1HN],15N hetNOE values for Rev ARM in aqueous solution at pH 7.4 average 0.47 for residues T34–R50, consistent with a disordered peptide. In contrast, the hetNOEs of the Rev ARM peptide in complex with RRE StemIIB average 0.83 for residues T34–R50, and in 50% TFE average 0.77 for residues T34–R50. These higher hetNOE values indicate higher backbone rigidity and are typical of a well-ordered secondary structure.
RRE StemIIB it's the RNA binding Rev ARM.
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We further characterized the differences in IA and IIB binding modes using amide proton chemical shifts from 15N HSQC NMR spectra to monitor changes in the peptide-RNA interfaces. There is little peak dispersion of peptide resonances in the absence of RNA (Figure 5C), indicative of a largely unstructured molecule.
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
We further characterized the differences in IA and IIB binding modes using amide proton chemical shifts from 15N HSQC NMR spectra to monitor changes in the peptide-RNA interfaces. There is little peak dispersion of peptide resonances in the absence of RNA (Figure 5C), indicative of a largely unstructured molecule. However, we observe substantial amide peak dispersion in the presence of either IIB (red) or IA (blue) RNAs (Figure 5C), including the Hε protons of arginine side chains (Figure 5C inset). The overall upfield shifts observed in both 1H and 15N dimensions is consistent with stabilization of peptide α-helical structure upon binding (Wang and Jardetzky, 2002).
Protein: DP03528 (UniProt P69718)
Region: residues 34	to 50
Annotation: RNA binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Given, the purine-rich internal loop of IA, we asked if this amino acid also is essential for IA binding. Interestingly, mutation of Asn40 had no effect on IA binding. Conversely, mutation of Arg41, which does not affect IIB binding (Tan et al., 1993), showed a reproducible 2-fold decrease in IA affinity (Figure 5A). R38A and R46A mutants showed similar 2-fold reductions in IA affinity but had no effect on IIB, while R43A, R44A, and W45A mutants bound IA like the wild type peptide. Helical wheel projections clearly show that different surfaces of the helix are used to recognize IIB and IA RNAs (Figure 5B).
Protein: DP03528 (UniProt P69718)
Region: residues 35	to 50
Annotation: protein localization to nucleoplasm (Biological process)
Evidence: green fluorescent protein fusion protein localization evidence used in manual assertion
Supporting statements:
Rev–GFP showed typical predominantly nuclear localization (>80% of fluorescence) (Fig. 2A). In contrast, RevM5–GFP fluorescence was apparent mainly in the cytoplasm, with less than 22% of total fluorescence in the nucleus (Fig. 2A).
RevM5 has a mutation in this IDR.
Protein: DP03528 (UniProt P69718)
Region: residues 35	to 46
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
As shown in a gel mobility shift assay (Figure 2), the addition of Rev normally leads to formation of multimeric complexes with 35S-labelled RRE.
Protein: DP03528 (UniProt P69718)
Region: residues 35	to 46
Annotation: protein binding (Molecular function)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
The experiment demonstrates the specificity of the Rev-importin-β interaction, as importin-β did not bind to the GST-Rev NLS mutant, or to GST protein. This was an unexpected finding, and identifies Rev as the first protein known to contain an NLS specific for the 97 kDa importin-β receptor, and not importin-α.
Protein: DP03529 (UniProt Q9NP98)
Region: residues 1	to 174
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results, demonstrating the intrinsically disordered/ensemble-state nature of N-FATZ-1 and Δ91-FATZ-1, are further supported by the 1H-15N heteronuclear single-quantum coherence (HSQC) spectra recorded for both constructs, which display a narrow chemical shift range in the proton dimension, as is typical for IDR-containing proteins (fig. S5A).
Cross-references: BMRB:50496
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results, demonstrating the intrinsically disordered/ensemble-state nature of N-FATZ-1 and Δ91-FATZ-1, are further supported by the 1H-15N heteronuclear single-quantum coherence (HSQC) spectra recorded for both constructs, which display a narrow chemical shift range in the proton dimension, as is typical for IDR-containing proteins (fig. S5A).
Cross-references: BMRB:50497
Protein: DP03529 (UniProt Q9NP98)
Region: residues 1	to 174
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We further characterized N-FATZ-1 and Δ91-FATZ-1 using SEC combined with SAXS. The resulting scattering profiles and dimensionless Kratky plots are characteristic of intrinsically disordered proteins (IDPs), and subsequent modeling indicates that both constructs are best described as a conformational ensemble (Fig. 1, F to J, and Supplementary Results) (32). In addition, we derived the radius of gyration (Rg) of N-FATZ-1 and Δ91-FATZ-1 from analysis of SAXS data (table S2) and obtained Rg/Rh ratios of 1.1 to 1.2 that are, once again, consistent with the presence of IDRs (33).
Cross-references: SASBDB:SASDJJ6
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We further characterized N-FATZ-1 and Δ91-FATZ-1 using SEC combined with SAXS. The resulting scattering profiles and dimensionless Kratky plots are characteristic of intrinsically disordered proteins (IDPs), and subsequent modeling indicates that both constructs are best described as a conformational ensemble (Fig. 1, F to J, and Supplementary Results) (32). In addition, we derived the radius of gyration (Rg) of N-FATZ-1 and Δ91-FATZ-1 from analysis of SAXS data (table S2) and obtained Rg/Rh ratios of 1.1 to 1.2 that are, once again, consistent with the presence of IDRs (33).
Cross-references: SASBDB:SASDJK6
Protein: DP03529 (UniProt Q9NP98)
Region: residues 1	to 174
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The calculation of the compaction index using hydrodynamic radius (Rh) values derived from size exclusion chromatography (SEC) combined with dynamic light scattering (DLS) and viscometry measurements (table S1) (31), together with the analysis of the 222/200 ellipticity ratio, indicated a premolten globule for N-FATZ-1 and an increased content of regular secondary structure for Δ91-FATZ-1.
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The calculation of the compaction index using hydrodynamic radius (Rh) values derived from size exclusion chromatography (SEC) combined with dynamic light scattering (DLS) and viscometry measurements (table S1) (31), together with the analysis of the 222/200 ellipticity ratio, indicated a premolten globule for N-FATZ-1 and an increased content of regular secondary structure for Δ91-FATZ-1.
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: actinin binding (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
In relation to the binding of the shorter FATZ-1 constructs, we could not detect complex formation between N-FATZ-1 and rod-α-actinin-2 (Fig. 2C), while Δ91-FATZ-1 formed 2:1, 2:1, and 1:1 complexes with α-actinin-2, rod-α-actinin-2, and hd-α-actinin-2, respectively (Fig. 2D, fig. S6, B and C, and table S1).
In SEC-MALS, we also observed a 2:1 complex between Δ91-FATZ-1 and human (nonmuscle) α-actinin-1 (fig. S6D and table S1).
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: actinin binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We used isothermal titration calorimetry (ITC) to quantify the interaction affinity. N-FATZ-1 did not interact with rod-α-actinin-2, whereas Δ91-FATZ-1 showed a strong 2:1, 2:1, and 1:1 interaction with α-actinin-2 dimer, dimeric rod-α-actinin-2, and hd-α-actinin-2, respectively, in agreement with SEC-MALS data (Fig. 2, F to H, fig. S6E, and table S3).
Protein: DP03529 (UniProt Q9NP98)
Region: residues 92	to 299
Annotation: actinin binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
We next designed the “fiveE” Δ91-FATZ-1 mutant, based on sequence alignment and metastructure analysis of FATZ proteins, in which five conserved positively charged residues within the CTR were reverted to negatively charged glutamates (K182E+R190E+K217E+K219E+R223E; see Methods). This construct did not form a stable complex with α-actinin-2 as assessed by SEC-MALS (Fig. 2E), in agreement with a very low ITC signal and for which a Kd could not be determined (see Fig. 2I and table S3).
Protein: DP03529 (UniProt Q9NP98)
Region: residues 119	to 237
Annotation: actinin binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
LP-MS revealed a protected (i.e., interacting) Δ91-FATZ-1 region spanning residues 119 to 237 (fig. S8). XL-MS, which was performed using a zero-length cross-linker, revealed three specific cross-links, K383/D205, E567/K233, and D893/K176 (see fig. S9; α-actinin-2 residues in italics), supporting the interaction between the CTR of FATZ-1 and the rod of α-actinin-2 (fig. S6E).
Protein: DP03529 (UniProt Q9NP98)
Region: residues 176	to 292
Annotation: actinin binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We could not fully assign Δ91-FATZ-1 due to fast relaxation of cross-peaks in the region comprising residues 177 to 291. We could, however, locate the α-actinin-2–interacting region within the CTR at residues 176 to 292, as the corresponding cross-peaks disappeared or showed a drop in signal intensity (Fig. 2J and fig. S5B). We found a similar signal reduction pattern and thus binding behavior for both α-actinin-2 and hd-α-actinin-2. Further, a decrease in signal intensity upon binding to α-actinin-2 around residues 106 and 128, mapping to the GRR, indicated additional binding site(s) apart from the interacting region found within the CTR, which is in line with ITC and peptide array data (Fig. 2K and figs. S6 and S7).