LiteFold/DisProt huggingface dataset:
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 72
Annotation: evasion of host immune response (Biological process)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
Conversely, increasing the concentration of Tat protein, while maintaining a fixed concentration of eIF2, resulted in a marked reduction in eIF2 phosphorylation (lanes 5-8). These data suggest that Tat and eIF2 can compete as substrates for phosphorylation by autophosphorylated PKR. Considering the relative molecular masses of Tat and eIF2 (about 10 and 125 kDa, respectively), they appear to serve as substrates for PKR and as competitors on a comparable molar basis.
Activation of PKR by dsRNA is accompanied by autophosphorylation. When activated PKR catalyzes the phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2), which results in the sequestration of a second initiation factor, the guanosine nucleotide exchange factor eIF2B, leading to the inhibition of protein synthesis. This mode of translational shut down constitutes a host defense mechanism and, as such, is detrimental to the viral life cycle. The avoidance of the activation of PKR and/or eIF2 proteins serves as a viral strategy to circumvent this host response.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 72
Annotation: evasion of host immune response (Biological process)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
In the absence of Tat, PKR was autophosphorylated in a dsRNA-dependent fashion (lanes 1 and 2). Preincubation of PKR with increasing concentrations of purified Tat-72 prior to the addition of dsRNA eliminated PKR autophosphorylation (lanes 3 and 4). As in previous experiments (Figs. 2, 3, 4, 5), when the addition of Tat was delayed until after PKR activation by dsRNA had occurred, both Tat and PKR were phosphorylated (lane 5). These observations indicate that Tat-72 can inhibit the activation of PKR by dsRNA in vitro, as well as its activity in phosphorylating eIF2.
Activation of PKR by dsRNA is accompanied by autophosphorylation. When activated PKR catalyzes the phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2), which results in the sequestration of a second initiation factor, the guanosine nucleotide exchange factor eIF2B, leading to the inhibition of protein synthesis. This mode of translational shut down constitutes a host defense mechanism and, as such, is detrimental to the viral life cycle. The avoidance of the activation of PKR and/or eIF2 proteins serves as a viral strategy to circumvent this host response.
Protein: DP00929 (UniProt P04608)
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).
The authors describe an HIV-1 subtype B Tat protein that is 101 residues long (UniProtKB:P20879; DisProt:DP03560). However, since the regions 41-54 are 100% identical, this IDR is considered to be involved in the same function.
Protein: DP00929 (UniProt P04608)
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: DP00929 (UniProt P04608)
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: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3C, where GST-Tat, but not GST, was able to bind to 35S-labeled CBP in vitro.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: transcription coactivator binding (Molecular function)
Evidence: radioligand binding assay evidence used in manual assertion
Supporting statements:
The results of such an experiment are shown in Fig. 3C, where GST-Tat, but not GST, was able to bind to 35S-labeled CBP in vitro.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: transcription regulator activator activity (Molecular function)
Evidence: transcriptional activation assay evidence used in manual assertion
Supporting statements:
Tat is one of the most powerful viral activators known to date. Tat could stimulate transcription of HIV-1 promoter anywhere from 100- to 1000-fold depending on the assay conditions used.
Taken together, the transient transfection results indicate that neither K50 nor K51 mutations alone are sufficient to completely lose the Tat transactivation on HIV-1 LTR.
Figure 5 shows the transcription activator activity of the wild-type TAT protein.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: protein binding (Molecular function)
Evidence: radioisotope assay evidence used in manual assertion
Supporting statements:
When binding 35S-labeled Tat to various GST-p300 domains, we found that Tat bound stably to all A, B, and C mutant domains under 0.1 M salt wash conditions (Fig. 4B, lanes 1-4).
Protein: DP00929 (UniProt P04608)
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: DP00929 (UniProt P04608)
Region: residues 42	to 54
Annotation: RNA polymerase core enzyme binding (Molecular function)
Evidence: qualitative western immunoblotting 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.
Protein: DP00929 (UniProt P04608)
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: DP00929 (UniProt P04608)
Region: residues 42	to 54
Annotation: nucleosome 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. 7B, where acetylated Tat peptide was able to bind to core histones. It is interesting to note that core histones in the absence of DNA did not bind to acetylated Tat, indicating that a fixed conformation of nucleosome is required for Tat to bind to core histones.
Experiments show that the wild-type not acetylated peptide also binds nucleosomes but in a lesser degree.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: histone acetyltransferase binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
As shown in Fig. ​1c, wild-type 101 and 86 Tat proteins bound the HAT activity present in the nuclear extract with similar efficiencies.
Protein: DP00929 (UniProt P04608)
Region: residues 49	to 57
Annotation: histone acetyltransferase binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
As shown in Fig. 1c, wild-type 101 and 86 Tat proteins bound the HAT activity present in the nuclear extract with similar efficiencies. The affinity was only slightly decreased in mutants Tat 86 Δ(1–21) and Tat 86C(22–27)A. On the contrary, amino acid substitutions of the arginines in the arginine-rich domain almost abolished association of Tat with the HAT activity.
Protein: DP00929 (UniProt P04608)
Region: residues 1	to 86
Annotation: transcription regulator activator activity (Molecular function)
Evidence: chromatin immunoprecipitation-PCR evidence used in manual assertion
Supporting statements:
After Tat treatment, a remarkable enrichment for this genomic region (10-fold for p300 and 33-fold for CBP) was observed (Fig. ​4e). These data demonstrate that Tat-mediated activation of the integrated LTR in vivo is concomitant with the recruitment of p300 and CBP specifically to the promoter region.
Protein: DP00929 (UniProt P04608)
Region: residues 48	to 57
Annotation: histone acetyltransferase binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Only fusion proteins which contained the Tat basic domain (residues 48 to 57) bound p300, including a fusion protein that expressed only this basic domain region (Fig. 4A, top).
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H–15N HSQC spectrum of H6-hBASP1 shows a very narrow peak dispersion in the 1H dimension typical for intrinsically disordered proteins (Fig. 1).
Secondary chemical shifts for 13C′, 13Cα, 1Hα (Fig. 3) show only minor deviations from random coil chemical shift values.
Cross-references: BMRB:18417
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 227
Annotation: protein homooligomerization (Biological process)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
 Under 150 mM NaCl and neutral pH conditions, NAP-22 samples showed two bands after SDS-PAGE. The lower band of ∼50 kDa was considered the monomer (Fig. 1A, white arrow). Another band that showed low mobility in the 10 % acrylamide gel was judged to be the oligomer (Fig. 1A, black arrow). Enlargement of the oligomer band showed that the band was composed of many bands of various number of monomers (Fig. 1B and C, Fig. 2A)
The dose-dependent effect of NaCl or MgCl2 on oligomerization was evident at 37℃ and pH 7.4 (Fig. 1B and C).
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 227
Annotation: calmodulin binding (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Further addition of calmodulin (CaM) abolished oligomer formation and the formation of 1:1 complex of CaM and NAP-22 was observed (arrow in Fig. 1D) [11]. Addition of CaM after oligomerization also diminished oligomer.
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 67
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Further addition of calmodulin (CaM) abolished oligomer formation and the formation of 1:1 complex of CaM and NAP-22 was observed (arrow in Fig. 1D) [11]. Addition of CaM after oligomerization also diminished oligomer.
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 227
Annotation: supramolecular fiber organization (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Observed NAP-22 oligomers are shown in Fig. 4. NAP-22 oligomers formed in HMEN buffer without lipid addition (CTL) showed a tangled rope-like filamentous structure.
Morphological analysis showed the formation of tangled rope-like filaments in the absence of lipid (Fig. 4). The presence of many annular structures in the filaments suggested that these rings could be the oligomer that assembled to make rope-like filaments.
The ring-structures observed on the NAP-22 aggregates observed in the presence of CL or PUFA were looked like ellipsoidal, and the size of the annular oligomers were slightly larger than that of oligomers formed in the absence of lipid (CTL). This suggests that CL and PUFA could increase the monomer number in the oligomer.
These results suggest the participation of NAP-22 to liquid-liquid phase separation through oligomerization.
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Our observations clearly indicate that the N-terminal region of BASP1 transiently samples compact substrates despite the lack of significant secondary 13C backbone chemical shifts for that regions.
Protein: DP00930 (UniProt P80723)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The PRE correlation matrix points to the existence of partially folded structural segments comprising residues 1–70, 70–90, 90–140 and, 170–200 with the N-terminus being the most compact one. Inter-segmental couplings are weak or even anti-correlated. These findings are in very good agreement with earlier studies providing evidence for an N-terminal compaction of BASP1 in solution, while the rest of the polypeptide chain displays random coil characteristics.
Protein: DP00931 (UniProt Q5ZYC9)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
During purification, IcmR is slowly digested by an endogenous bacterial protease to form a smaller fragment that can account for ∼30-40% of the sample (Experimental Procedures, Figure 1C, lane 1).
This complex was trypsinized to remove flexible residues from the two proteins.
Protein: DP00931 (UniProt Q5ZYC9)
Region: residues 87	to 120
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
This complex was trypsinized to remove flexible residues from the two proteins. 
During purification, IcmR is slowly digested by an endogenous bacterial protease to form a smaller fragment that can account for ∼30-40% of the sample (Experimental Procedures, Figure 1C, lane 1).
Protein: DP00931 (UniProt Q5ZYC9)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
After refinement, the final model consists of residues 28–86 of IcmR and residues 1–191 of IcmQ (see Table 1).
Cross-references: PDB:4EYY
Protein: DP00931 (UniProt Q5ZYC9)
Region: residues 87	to 120
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
After refinement, the final model consists of residues 28–86 of IcmR and residues 1–191 of IcmQ (see Table 1).
Cross-references: PDB:4EYY
Protein: DP00932 (UniProt P35926)
Region: residues 1	to 76
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity.
Electron density for the N-terminal 76 residues was absent, indicating that it may be a flexible element.
Cross-references: PDB:3PLW
Protein: DP00932 (UniProt P35926)
Region: residues 1	to 76
Annotation: enzyme activator activity (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
To test the functional importance of the N terminus, we constructed a deletion mutant of Ref that lacked the 76 N-terminal amino acids and purified it. It proved to be devoid of Ref-mediated nuclease activity on ssDNA under normal reaction conditions (Fig. 7, lanes 11–13). Some RecA-dependent ssDNA cleavage was seen at much higher concentrations of the mutant Ref protein (10× and 100×; Fig. 7, lanes 14–21). Ref ΔN76 was completely deficient in DNA binding to a 50-mer oligonucleotide up to a concentration of 2.4 μm using the assay shown in Fig. 1 (data not shown). This indicates that the disordered N-terminal domain plays an essential role the DNA binding activity of Ref and also enhances the RecA-dependent nuclease activity. We note that these N-terminal 76 amino acid residues represent a very highly charged part of the protein.
Protein: DP00932 (UniProt P35926)
Region: residues 1	to 76
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
To test the functional importance of the N terminus, we constructed a deletion mutant of Ref that lacked the 76 N-terminal amino acids and purified it. It proved to be devoid of Ref-mediated nuclease activity on ssDNA under normal reaction conditions (Fig. 7, lanes 11–13). Some RecA-dependent ssDNA cleavage was seen at much higher concentrations of the mutant Ref protein (10× and 100×; Fig. 7, lanes 14–21). Ref ΔN76 was completely deficient in DNA binding to a 50-mer oligonucleotide up to a concentration of 2.4 μm using the assay shown in Fig. 1 (data not shown). This indicates that the disordered N-terminal domain plays an essential role the DNA binding activity of Ref and also enhances the RecA-dependent nuclease activity. We note that these N-terminal 76 amino acid residues represent a very highly charged part of the protein.
Protein: DP00934 (UniProt P61925)
Region: residues 14	to 33
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The first a-helical region from residues 7 to 13 corresponds to the high affinity binding helix seen in the crystal structure. The second helix is from residue 34 to 43 of PKIa, and overlaps with the Nuclear Export Signal of PKIa. The remainder of PKIa is not structured. The experiments were done with the rabbit PKIa (Uniprot P61926), IDR is 100% identical.
Protein: DP00934 (UniProt P61925)
Region: residues 44	to 76
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The first a-helical region from residues 7 to 13 corresponds to the high affinity binding helix seen in the crystal structure. The second helix is from residue 34 to 43 of PKIa, and overlaps with the Nuclear Export Signal of PKIa. The remainder of PKIa is not structured. The experiments were done with the rabbit PKIa (Uniprot P61926), IDR is 100% identical.
Protein: DP00936 (UniProt O88998)
Region: residues 339	to 352
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A large portion, 209 residues of a total of 463 residues for the mature full-length protein, is missing in the electron density most likely due to α-chymotrypsin treatment of Olfm1. The final model consists of residues Val211–Phe477 and Arg210–Ala480 (the last two alanines Ala479 and Ala480 are from the NotI restriction site) for chains A and B, respectively, excluding loops Ala339–His352 in both chains.
Cross-references: PDB:5AMO
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 515
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We show that this small protein presents two subdomains linked by an 11-residue linker, with the N-subdomain lacking a well-defined conformation.
To supplement the structural characterisation of PX, we measured heteronuclear relaxation at 600 MHz. Of the 95 amino acid residues (474–568), 68 {1H}-15N nOes (Fig. 3), 68 R1 and 68 R2 (data not shown) could be measured. The resulting data confirm that residues 474–515 indeed present differential dynamic behaviour compared to residues 516–568. In particular, the {1H}-15N nOe reveals a rigid domain (516–568) linked to a flexible domain (474–504) by an even more flexible linker (505–515).
Cross-references: PDB:1R4G
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 515
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This model is validated by experimental RDCs and SAXS data measured from PX from Sendai virus, a molecule containing folded and unfolded domains, confirming both local conformational sampling and the average size and shape of the ensemble. Despite the highly disperse ensemble, regions of preferential structuring along the flexible chain of PX are detected.
In this study, experimental RDCs and SAXS data are combined with a conformational sampling algorithm to develop a structural model of the 57-aa unfolded domain of PX. Although they cover a smaller range than the RDCs measured in the folded domain, the N-NH and C′-NH RDC measured for PX aligned in 5% of C12E6/hexanol nevertheless present identifiable fine structure and values that are non-negligible compared with the folded domain.
57-aa including the 15 residues of the His-tag.
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 517
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The assignment of this small protein has been made difficult due to the limited amount of regular secondary structure (the N-terminus before Pro58 is disordered) shown by chemical shift data and the absence of medium and long-range NOEs.
An isotopically 15N/13C double-labelled sample of the X protein spanning amino acids 474 to 568 of the phosphoprotein (accession number swiss-prot P04859) (corresponding respectively to residue 15 and 109 in our numbering scheme) was obtained from 4 L E. coli BL21 (DE3) culture in M9 minimal medium containing 1 g/l 15NH4Cl and 1 g/l 13C6-glucose as sole nitrogen and carbon sources.
Cross-references: BMRB:4999
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 517
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The assignment of this small protein has been made difficult due to the limited amount of regular secondary structure (the N-terminus before Pro58 is disordered) shown by chemical shift data and the absence of medium and long-range NOEs. This suggests that a flexible linker is needed between the oligomerisation domain/polymerase binding site and the N-RNA binding domain for biological activity.
Cross-references: BMRB:4999
Protein: DP00939 (UniProt P04859)
Region: residues 474	to 518
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 (A) Overall rotational correlation time τc. Isotropic rotational diffusion with a correlation time of 7.3 ns was assumed for the structured part (519–568), whereas a local diffusion model was used for residues in the unstructured part.
Isotope-labeled samples of the PX domain (474–568) of SeV phosphoprotein P, including an N-terminal His tag and a factor Xa cleavage site (MRGSHHHHHHIEGR), were prepared as described previously (30).
All amide protons in the N-terminal part of PX exchanged within the dead time confirming the unstructured nature of this N-terminal subdomain.
From 474 to 518 is unstructured and from 519 to 568 structured.