LiteFold/DisProt huggingface dataset:
Protein: DP03549 (UniProt Q91H74)
Region: residues 2946	to 2961
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 in form 2 of the crystals obtained, indicating this residues were unstructured.
Cross-references: PDB:6KR3
Protein: DP03550 (UniProt Q703G9)
Region: residues 429	to 442
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density map of the IPNV SVP displays unambiguous density for most of the polypeptide chain, allowing the visualization of residues 6 to 428 of VP2, with a break in density between amino acids 110 to 117 at the distal tip of domain S, which appears disordered (Fig.11 and ​and2C).
Cross-references: PDB:3IDE
Protein: DP03551 (UniProt P22173)
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:
The crystal structure of the complex between full-length VP1 and VP3 was solved by molecular replacement using the structure of IPNV VP1 (9) as a search model and refined to a resolution of 2.2 Å with residual Rxpct = 0.179 and Rfree = 0.215 (Table 1). The final structure is of high stereochemical quality with 98% of the residues occupying the favored region of the Ramachandran plot. Three copies of VP1 are present in the asymmetric unit (AU) of the crystal, and electron density was observed from residues 27 to 792 for each chain of VP1 (no density was observed for residues 1 to 26 and 793 to 845).
Cross-references: PDB:3ZED
Protein: DP03551 (UniProt P22173)
Region: residues 793	to 845
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of the complex between full-length VP1 and VP3 was solved by molecular replacement using the structure of IPNV VP1 (9) as a search model and refined to a resolution of 2.2 Å with residual Rxpct = 0.179 and Rfree = 0.215 (Table 1). The final structure is of high stereochemical quality with 98% of the residues occupying the favored region of the Ramachandran plot. Three copies of VP1 are present in the asymmetric unit (AU) of the crystal, and electron density was observed from residues 27 to 792 for each chain of VP1 (no density was observed for residues 1 to 26 and 793 to 845).
Cross-references: PDB:3ZED
Protein: DP03551 (UniProt P22173)
Region: residues 799	to 845
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Despite being crystallized in the presence of Mn2+ and ATP, no metal ions or nucleotides were observed at the active site. While additional electron density was seen connected to the C-terminus of the molecular replacement search model in three of the four copies of VP1 present in the asymmetric unit only eight additional residues (791–798) could be placed, suggesting that residues 799–845 are not ordered.
Cross-references: PDB:2YIB
Protein: DP03551 (UniProt P22173)
Region: residues 793	to 845
Annotation: viral genome replication (Biological process)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
Both full-length and ΔC55 VP1 yield RNA/DNA hybrids of various heterologous ssRNA templates, ΔC55 being roughly 5-fold more active than the full-length enzyme, while ΔN27C55 VP1 reverse transcriptase activity is extremely low (Table 1, Figure 4).
Protein: DP03551 (UniProt P22173)
Region: residues 20	to 30
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 this region when the protein is bound to the ions Mg+2, K+ and Cl- or only K+ and Cl-.
Cross-references: PDB:2YI9
PDB:2YI8
Protein: DP03551 (UniProt P22173)
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:
The PDB shows disorder in this region when the protein is bound to the ions Mg+2, K+ and Cl- or only K+ and Cl-.
Cross-references: PDB:2YI9
PDB:2YI8
Protein: DP03552 (UniProt P10636-2)
Region: residues 1	to 352
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
All the profiles are featureless, and the Kratky plots [s2I(s) vs s] are without apparent peaks (Supporting Information Figure 3), which is typical for unfolded proteins.
Table 1 indicates that the larger constructs (ht23 and ht40) have Rg values close to or smaller than the predicted random coil values, which are shown by ref 29 to agree well with the experimental data from chemically unfolded proteins (note that as tau constructs are not denatured using chemicals the random coil estimations cannot be considered ideal predictions, but they do provide a useful guidance).
For full length constructs (ht40 and ht23), little difference from the pool distribution was observed (typical models of ht40 selected from the random pools are displayed in Figure 4 to demonstrate that the protein is indeed rather unstructured).
Protein: DP03553 (UniProt O94829)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure, some disordered stretches of residues at the N- and C-termini of Imp13, as well as a long inter-loop between HEAT 14 and 15 (residues 655–673) and a few residues in loops are missing in the final model; the full-length Ubc9 could be modelled.
Residues 1-18 and 656-673 are disordered in the structure.
Cross-references: PDB:2XWU
Protein: DP03553 (UniProt O94829)
Region: residues 656	to 673
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the structure, some disordered stretches of residues at the N- and C-termini of Imp13, as well as a long inter-loop between HEAT 14 and 15 (residues 655–673) and a few residues in loops are missing in the final model; the full-length Ubc9 could be modelled.
Residues 1-18 and 656-673 are disordered in the structure.
Cross-references: PDB:2XWU
Protein: DP03554 (UniProt Q9UKK9)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The experimental electron density map is of great quality except that the N-terminal 1–13 residues were disordered without electron density and therefore were omitted in the final model.
Cross-references: PDB:2DSB
PDB:2DSC
PDB:2DSD
Protein: DP03555 (UniProt Q8K310)
Region: residues 478	to 496
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As described below, the N-terminal segment spanning residues 478–496 adopted a disordered structure, which caused the missing backbone resonances.
Protein: DP03555 (UniProt Q8K310)
Region: residues 478	to 496
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As described below, the N-terminal segment spanning residues 478–496 adopted a disordered structure, which caused the missing backbone resonances.
Flexible linker connecting RRM1 and RRM2 of mouse Matrin-3.
Protein: DP03556 (UniProt P35813)
Region: residues 369	to 382
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two regions of polypeptide that are not visible in the electron density map are assumed to be disordered. These are residues 322-325, which connect the α-helices a7 and a8, and the C-terminal 18 residues.
The last 14 residues are disordered in the structure.
Cross-references: PDB:1A6Q
Protein: DP03557 (UniProt Q91AU0)
Region: residues 2223	to 2314
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
By contrast, the fragments consisting of D2 or/and D3 domains have far-UV CD spectra typical of proteins of being predominantly disordered, consistent with previous reports on NS5A D2 and D3 of other HCV isolates [36]–[39].
Protein: DP03557 (UniProt Q91AU0)
Region: residues 2331	to 2419
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
By contrast, the fragments consisting of D2 or/and D3 domains have far-UV CD spectra typical of proteins of being predominantly disordered, consistent with previous reports on NS5A D2 and D3 of other HCV isolates [36]–[39].
Protein: DP03557 (UniProt Q91AU0)
Region: residues 2331	to 2419
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Remarkably, as shown in Figure 3c, addition of D3 sample not only induced the disappearance of almost the same set of HSQC peaks as induced by NS5A(300–447), but also triggered significant shifts of many extra residues. This implies that the majority of the NS5A residues critical for binding VAPB are located on NS5A-D3.
Protein: DP03557 (UniProt Q91AU0)
Region: residues 2331	to 2419
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The recombinant 89-residue NS5A-D3 protein has a far-UV CD spectrum (Figure 4a) typical of highly-unstructured proteins, consistent with previous reports on NS5A-D3 of other HCV isolates [38], [39]. This conclusion is further evident from the very narrow 1H-(1.8 ppm) and 15N-(19.5 ppm) spectral dispersions of its HSQC spectrum (Figure 4b), which also indicate the absence of a tight tertiary packing in D3.
Protein: DP03557 (UniProt Q91AU0)
Region: residues 2379	to 2398
Annotation: protein sequestering activity (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
These results thus suggest that in the pre-existence of D3B, EphA4 at low concentration is not able to bind to VAPB-MSP but at high concentrations, EphA4 will start to displace the D3B peptide from binding with the MSP fold. Therefore, NS5A does compete with EphA4 in binding with VAPB-MSP.
Protein: DP03558 (UniProt P04591)
Region: residues 110	to 148
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker regions in ΔGag exhibit low 15N-{1H} heteronuclear NOE values, close to zero 1DNH RDC values, and nearly random coil chemical shifts (Fig. 4, Table S3, and Fig. S2), indicative of intrinsic disorder and high mobility such that the ordered structural domains are like beads on a string. These regions include the large stretch of residues connecting MA to CA (residues 110–148), the C-terminal tail of CA (residues 353–363) and the SP1 region that connects CA to the N-terminal zinc-knuckle of NC (residues 364–377), and the linker (residues 408–412, especially residues 411 and 412) that connects the N- and C-terminal zinc knuckles of NC. Overall, these flexible, solvent exposed regions are primarily responsible for extreme sensitivity of Gag to proteolysis and conformational heterogeneity that precludes crystallization.
Protein: DP03558 (UniProt P04591)
Region: residues 353	to 363
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker regions in ΔGag exhibit low 15N-{1H} heteronuclear NOE values, close to zero 1DNH RDC values, and nearly random coil chemical shifts (Fig. 4, Table S3, and Fig. S2), indicative of intrinsic disorder and high mobility such that the ordered structural domains are like beads on a string. These regions include the large stretch of residues connecting MA to CA (residues 110–148), the C-terminal tail of CA (residues 353–363) and the SP1 region that connects CA to the N-terminal zinc-knuckle of NC (residues 364–377), and the linker (residues 408–412, especially residues 411 and 412) that connects the N- and C-terminal zinc knuckles of NC. Overall, these flexible, solvent exposed regions are primarily responsible for extreme sensitivity of Gag to proteolysis and conformational heterogeneity that precludes crystallization.
Protein: DP03558 (UniProt P04591)
Region: residues 364	to 377
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The linker regions in ΔGag exhibit low 15N-{1H} heteronuclear NOE values, close to zero 1DNH RDC values, and nearly random coil chemical shifts (Fig. 4, Table S3, and Fig. S2), indicative of intrinsic disorder and high mobility such that the ordered structural domains are like beads on a string. These regions include the large stretch of residues connecting MA to CA (residues 110–148), the C-terminal tail of CA (residues 353–363) and the SP1 region that connects CA to the N-terminal zinc-knuckle of NC (residues 364–377), and the linker (residues 408–412, especially residues 411 and 412) that connects the N- and C-terminal zinc knuckles of NC. Overall, these flexible, solvent exposed regions are primarily responsible for extreme sensitivity of Gag to proteolysis and conformational heterogeneity that precludes crystallization.
Protein: DP03558 (UniProt P04591)
Region: residues 133	to 145
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In intact ΔGag, the N-terminal residues of CA (residues 133–145) are intrinsically disordered and exhibit narrow chemical shift dispersion (see above and Fig. S2). As proteolysis of ΔGag proceeds, new 1HN/15N cross-peaks appear in the spectrum and grow in intensity with time (Fig. 5A). A few of these can be readily assigned by reference to the spectrum of isolated CA. Among these Ile134, Val135, Asn137, Gly140, Met142, Val143, His144, and Gln145 are directly involved in the formation of the β-hairpin (residues 133–145) and exhibit completely different chemical shifts (labeled in blue in Fig. 5A) compared with their unstructured counterparts.
Protein: DP03558 (UniProt P04591)
Region: residues 133	to 145
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As proteolysis of ΔGag proceeds, new 1HN/15N cross-peaks appear in the spectrum and grow in intensity with time (Fig. 5A). A few of these can be readily assigned by reference to the spectrum of isolated CA. Among these Ile134, Val135, Asn137, Gly140, Met142, Val143, His144, and Gln145 are directly involved in the formation of the β-hairpin (residues 133–145) and exhibit completely different chemical shifts (labeled in blue in Fig. 5A) compared with their unstructured counterparts.
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The main difficulty in determining the NMR Tat structure was to resolve the sequential assignment [23]. This was due to the high number of peak overlaps in the homonuclear 1H NMR spectra, repetitive sequences and the presence of 11 prolines.
This could be due to the absence of α-helix and β-sheet and the flexibility of the Tat backbone, which induces the poor dispersion of our NMR spectra. However, the nanomolar activities observed with Tat indicate that Tat certainly has a conserved folding. We identified 272 long-range NOEs that would have almost disappeared with a random coil. The long-range NOEs, observed with almost each residue (figure 6), suggest a certain stability of our structure compared to the one studied by Bayer et al.
Cross-references: PDB:1JFW
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: viral gene expression (Biological process)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
The Tatwt construct did indeed result in a high level of luciferase expression (Fig. 1C). The TatY26A variant showed an approximately 4-fold-reduced luciferase level, which confirms that the Y26A mutation significantly reduces Tat activity. In agreement with their inability to produce functional Tat protein, the Tatstop and Tatfs constructs resulted in very low luciferase levels that are indistinguishable from the background level obtained upon cotransfection of a control plasmid instead of HIV-rtTA.
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: regulatory region RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The six synthetic Tat proteins can bind to TAR RNA (Fig.3) and can inhibit PKR (data not shown).
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffer (Fig. 4 A), it can be deduced from the intensity of the negative 200 nm band that nonorganized structures are predominant (29). TableI reveals that there is no α helix in aqueous buffer excepted for Tat Mal and Tat Z2, which could have a short helix of eight to nine residues.
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: viral gene expression (Biological process)
Evidence: beta-galactosidase reporter gene assay evidence used in manual assertion
Supporting statements:
In each case, Tat was added to the cell buffer, and therefore expression of β-gal up to the control means that the synthetic Tat was able to cross the cytoplasmic and nucleus membranes, bind TAR, and interact with cellular cofactors.
Tat Bru can trans-activate HIV-1 LTR whereas Tat Oyi cannot, but they are both phosphorylated by PKR.
At 10 μm, the six Tat were showing levels of trans-activation so high that it was impossible to see differences between them because there was saturation.
Protein: DP03559 (UniProt P04610)
Region: residues 1	to 86
Annotation: viral gene expression (Biological process)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
At 10 μm, the six Tat were showing levels of trans-activation so high that it was impossible to see differences between them because there was saturation.
Protein: DP03560 (UniProt P20879)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffer (Fig. 4 A), it can be deduced from the intensity of the negative 200 nm band that nonorganized structures are predominant (29). TableI reveals that there is no α helix in aqueous buffer excepted for Tat Mal and Tat Z2, which could have a short helix of eight to nine residues.
Protein: DP03560 (UniProt P20879)
Region: residues 1	to 101
Annotation: regulatory region RNA binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The K d values vary from approximately 50 nm for both Tat Eli and Tat Mal to about 140 nmfor Tat Oyi and Tat JR. 
The six synthetic Tat proteins can bind to TAR RNA (Fig.3) and can inhibit PKR (data not shown).
Protein: DP03560 (UniProt P20879)
Region: residues 1	to 101
Annotation: viral gene expression (Biological process)
Evidence: beta-galactosidase reporter gene assay evidence used in manual assertion
Supporting statements:
In each case, Tat was added to the cell buffer, and therefore expression of β-gal up to the control means that the synthetic Tat was able to cross the cytoplasmic and nucleus membranes, bind TAR, and interact with cellular cofactors.
At 10 μm, the six Tat were showing levels of trans-activation so high that it was impossible to see differences between them because there was saturation.
Protein: DP03560 (UniProt P20879)
Region: residues 1	to 101
Annotation: viral gene expression (Biological process)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
At 10 μm, the six Tat were showing levels of trans-activation so high that it was impossible to see differences between them because there was saturation.
Protein: DP03560 (UniProt P20879)
Region: residues 41	to 54
Annotation: trans-activation response element binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3A, where wild-type peptide 41-54 was capable of binding to TAR RNA (lane 3).
Protein: DP03560 (UniProt P20879)
Region: residues 41	to 54
Annotation: acetylation display site (Disorder function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 1C, where Tat 41-54
peptide, but not 41-50 peptide (lanes 7±10), was acetylated with GST-HAT.
Protein: DP03560 (UniProt P20879)
Region: residues 41	to 54
Annotation: negative regulation of RNA binding (Biological process)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3A, where wild-type peptide 41-54 was capable of binding to TAR RNA (lane 3). The TAR RNA binding is completely abolished when lysines 50 and 51 are acetylated (lanes 6 and 7). We observed no binding of double-acetylated 50 and 51 peptide to TAR RNA at any peptide concentration (data not shown). Similar results were also observed when Tat protein was acetylated with GST-HAT prior to TAR RNA binding (Fig. 3B, lanes 4 and 5).
Protein: DP03560 (UniProt P20879)
Region: residues 42	to 54
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
Protein: DP03560 (UniProt P20879)
Region: residues 42	to 54
Annotation: transcription coactivator binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
Protein: DP03560 (UniProt P20879)
Region: residues 42	to 54
Annotation: cyclin binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 7A, where 35Slabeled TBP, CBP, and cyclin T could efficiently bind to wild-type but not acetylated 42-50 peptide.
Protein: DP03560 (UniProt P20879)
Region: residues 42	to 54
Annotation: RNA polymerase core enzyme binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Results from Western blots indicated that wild-type and not acetylated peptide was capable of binding to core-Pol II.