LiteFold/DisProt huggingface dataset:
Protein: DP00986 (UniProt Q8QWD4)
Region: residues 2	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
According to the PDB structures, the region within the boundaries is disordered.
Cross-references: PDB:4WM7
PDB:4WM8
Protein: DP00987 (UniProt A0A0H3CFC9)
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:
The anti-σ factor, NepR, contains 68 amino acids; electron density for the first 29 N-terminal residues and the last 6 residues of the C terminus is not visible in our maps.
The region the authors mention corresponds to the 1-22 region of this Uniprot.
Cross-references: PDB:3T0Y
Protein: DP00989 (UniProt P0ACX9)
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 this paper, we have shown that YdiE from E. coli has a highly similar structure, with a relatively large, unfolded N-terminal region and a C-terminal region that dimerizes through a highly hydrophobic interface.
Cross-references: PDB:4YNX
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
We also assessed the secondary structure of the NPBP peptide by circular dichroism (CD) spectroscopy, which revealed that NPBP and truncations of NPBP are intrinsically disordered in solution.
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We solved the crystal structure of the VP35 NPBP/ΔNPNTD complex to 3.7 Å resolution by selenomethionine single wavelength anomalous dispersion (Se-SAD) and observed four NPBP/ΔNPNTD heterodimers in the asymmetric unit (termed molA, molB, molC, and molD for ΔNPNTD and molE, molF, molG, and molH for NPBP) (Figure 2D, Figure S3A and Table S1).
In the structure of molG/molC, NPBP interacts exclusively with the foot lobe of ΔNPNTD. NPBP forms two orthogonal helices (VP35 residues 26–36 form an alpha helix and residues 40–42 form a turn of a 310 helix) and makes multiple hydrogen bonds and non-bonded contacts with NP (Figure 3B–E).
Cross-references: PDB:4YPI
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
These results revealed that VP35 residues 20–48 (i.e. NPBP) comprise the most critical region for high affinity ΔNPNTD binding (KD=18.0 ± 6.0 nM at 500 mM NaCl, Figure 2C and S2B; and KD=28.9 ± 6.4 nM at 150 mM NaCl, Figure S2C).
Further analysis of the ITC data and MALS results indicates that NPBP binds to ΔNPNTD with a 1:1 stoichiometry (Figure S2B) with a complex molecular weight corresponding to one molecule of ΔNPNTD and one molecule of NPBP (Figure S2D).
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Further analysis of the ITC data and MALS results indicates that NPBP binds to ΔNPNTD with a 1:1 stoichiometry (Figure S2B) with a complex molecular weight corresponding to one molecule of ΔNPNTD and one molecule of NPBP (Figure S2D).
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: viral transcription (Biological process)
Evidence: in vivo transcription assay evidence used in manual assertion
Supporting statements:
In contrast, residues 20–52 are critical for EBOV MG activity as N-terminal truncations that extend into this conserved region, including truncations such as in the 30–340 construct, resulted in >60% loss of activity relative to WT VP35 (residues 1–340). Deletion of the entire NPBP region plus the first 19 amino acids results in near-complete loss of MG activity, suggesting that the entire NPBP is required for activity.
Protein: DP00998 (UniProt Q05127)
Region: residues 26	to 36
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
NPBP forms two orthogonal helices (VP35 residues 26–36 form an alpha helix and residues 40–42 form a turn of a 310 helix) and makes multiple hydrogen bonds and non-bonded contacts with NP (Figure 3B–E).
Cross-references: PDB:4YPI
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: molecular sequestering activity (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
In these experiments, NPBP was titrated into the reaction while ssRNA and ΔNPNTD concentrations were held constant. Increasing NPBP concentration resulted in a proportional loss of ssRNA from the ssRNA-NP complex (Figure 5D), yielding an IC50 of 4 μM. These results indicate that ssRNA and NPBP binding to NP are mutually exclusive.
ΔNPNTD binds ssRNA and the ssRNA binding is inhibited by NPBP
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
In these experiments, NPBP was titrated into the reaction while ssRNA and ΔNPNTD concentrations were held constant. Increasing NPBP concentration resulted in a proportional loss of ssRNA from the ssRNA-NP complex (Figure 5D), yielding an IC50 of 4 μM. These results indicate that ssRNA and NPBP binding to NP are mutually exclusive.
ΔNPNTD binds ssRNA and the ssRNA binding is inhibited by NPBP
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: molecular sequestering activity (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In contrast to previous results for the peptide-free NP proteins (Figure 1B–C), which eluted at the V0, all NPBP-bound NP proteins eluted at a volume consistent with a well-behaved heterodimer (one molecule of NP and one NPBP molecule) (Figure 6C), indicating that NPBP interaction also prevents oligomerization.
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: molecular sequestering activity (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
These results revealed that VP35 residues 20–48 (i.e. NPBP) comprise the most critical region for high affinity ΔNPNTD binding (KD=18.0 ± 6.0 nM at 500 mM NaCl, Figure 2C and S2B; and KD=28.9 ± 6.4 nM at 150 mM NaCl, Figure S2C).
Further analysis of the ITC data and MALS results indicates that NPBP binds to ΔNPNTD with a 1:1 stoichiometry (Figure S2B) with a complex molecular weight corresponding to one molecule of ΔNPNTD and one molecule of NPBP (Figure S2D).
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: molecular sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We solved the crystal structure of the VP35 NPBP/ΔNPNTD complex to 3.7 Å resolution by selenomethionine single wavelength anomalous dispersion (Se-SAD) and observed four NPBP/ΔNPNTD heterodimers in the asymmetric unit (termed molA, molB, molC, and molD for ΔNPNTD and molE, molF, molG, and molH for NPBP) (Figure 2D, Figure S3A and Table S1).
In the structure of molG/molC, NPBP interacts exclusively with the foot lobe of ΔNPNTD. NPBP forms two orthogonal helices (VP35 residues 26–36 form an alpha helix and residues 40–42 form a turn of a 310 helix) and makes multiple hydrogen bonds and non-bonded contacts with NP (Figure 3B–E).
Cross-references: PDB:4YPI
Protein: DP00998 (UniProt Q05127)
Region: residues 20	to 48
Annotation: viral genome replication (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
VP35 NPBP inhibits Ebola RNA synthesis
To further test activity of NPBP in the context of EBOV infections, HeLa cells were pretransfected with the GFP-NPBP or GFP-control peptide constructs and then challenged with EBOV. Representative images of these infections show that GFP-NPBP, but not the GFP control plasmid was able to inhibit EBOV replication (Figure 7D). Consistent with the immunofluorescence results and with the MG assays, quantitative reverse transcription-PCR (qRT-PCR) results show that the presence of GFP-VP35 NPBP, but not the GFP-control, results in lower viral RNA in the cell supernatants (Figure 7E). Collectively, these results suggest that NPBP can functionally interact with the NP in the viral RDRP complex and has the potential to inhibit viral RNA synthesis.
Protein: DP01001 (UniProt B8YB65)
Region: residues 1	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The core of Rpo13 forms a HTH comprising helix-1 (α1; residues 38–56) and helix-2 (α2; residues 61–82) with the first visible Cα N-terminal residue (F33) facing the DNA-binding cleft (Figure 4B).
The PDB structure is about the archaeal RNA polymerase complex and involve many other proteins.
Cross-references: PDB:4AYB
Protein: DP01001 (UniProt B8YB65)
Region: residues 85	to 104
Annotation: double-stranded DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Finally, using EMSAs (Figure 6) we could readily detect interaction between purified recombinant Rpo13 and dsDNA with an apparent Kd of ∼2 µM, consistent with our NMR data (Figure 5B). We could not detect any significant single stranded DNA (ssDNA) binding activity (Figure 6A, left).
Deletion of the N-terminal tail rendered the protein prone to aggregation, but DNA binding was still detectable at low concentrations (Figure 6C, top). Importantly, however, deletion of the C-terminal tail (amino acids 85–104) had no detectable effect on protein stability or solubility but abrogated DNA binding (Figure 6C, below).
Protein: DP01001 (UniProt B8YB65)
Region: residues 83	to 104
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The core of Rpo13 forms a HTH comprising helix-1 (α1; residues 38–56) and helix-2 (α2; residues 61–82) with the first visible Cα N-terminal residue (F33) facing the DNA-binding cleft (Figure 4B).
The PDB structure is about the archaeal RNA polymerase complex and involve many other proteins.
Cross-references: PDB:4AYB
Protein: DP01001 (UniProt B8YB65)
Region: residues 1	to 104
Annotation: DNA-directed RNA polymerase complex (Cellular component)
Evidence: chromatin immunoprecipitation-chip evidence used in manual assertion
Supporting statements:
We also detect elevated signals of both proteins in some intragenic regions, perhaps indicative of polymerase pausing [an extensive genome-wide analysis will be published elsewhere (M.M. and S.D.B., unpublished data)]. Taken together, these data indicate that Rpo13 co-localizes with elongating RNAP.
The co-purification and crystallization of Rpo13 with RNAP clearly indicates a stable association in solution.
Protein: DP01001 (UniProt B8YB65)
Region: residues 47	to 52
Annotation: RNA polymerase binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues N47 and W51 with T48 and D52 of Rpo13’s α1 confer specificity for binding to the RNAP. The former amino acids bind to the Rpo5 subunit and the latter two to the clamp-head domain of Rpo1N. Two tryptophan residues, one from Rpo13 (W51) and the other from the clamp-head (W125) reciprocally dock via hydrogen bonds onto G60 of Rpo5 and T48 of Rpo13, respectively (Figure 4B). Further hydrogen bonds between Rpo13 N47 and P58 of Rpo5 and Rpo13 D52 and R124 of the clamp-head domain strengthen the binding of Rpo13 to the crevice formed by Rpo5 and the clamp head (Figure 4B).
Cross-references: PDB:4AYB
Protein: DP01001 (UniProt B8YB65)
Region: residues 1	to 32
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy in the far UV region on Rpo13 reveals a protein with ∼35% α-helical, 48% random coil and 17% beta-sheet content (Figure 5A, left; Supplementary Methods). This secondary structure assignment of Rpo13 in solution fits the X-ray secondary structural description of Rpo13 bound to the entire enzyme where only 39 residues out of 104 are ordered.
Protein: DP01001 (UniProt B8YB65)
Region: residues 83	to 104
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy in the far UV region on Rpo13 reveals a protein with ∼35% α-helical, 48% random coil and 17% beta-sheet content (Figure 5A, left; Supplementary Methods). This secondary structure assignment of Rpo13 in solution fits the X-ray secondary structural description of Rpo13 bound to the entire enzyme where only 39 residues out of 104 are ordered.
Protein: DP01001 (UniProt B8YB65)
Region: residues 1	to 104
Annotation: molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Full-length Rpo13 was also studied by NMR spectroscopy (Supplemental Methods). The 1H–15N–HSQC spectrum (Figure 5B) shows a poor dispersion in the proton chemical shift, indicating a loss in both secondary and tertiary structure. Interestingly, the analysis of the peaks cannot account for all residues (even considering signal overlap) and the spectrum is showing resonances for a subset of residues only. The missing peaks that include the tryptophan residue used for the specific interaction with Rpo1N, may have disappeared because of conformational exchange in the microsecond–millisecond timescale or because of segmental aggregation. This complex behaviour implies a molten globular structure that undergoes exchange between several conformations.
Protein: DP01002 (UniProt O87120)
Region: residues 53	to 70
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
(2Fo − Fc) and (Fo − Fc) maps showed that the N-termini of CdtA, CdtB, and CdtC started at residues 71, 23, and 25, respectively, indicating that the residues 53–70 of CdtA and residues 21–24 of CdtC are disordered in the crystal structure.
The most variable region is from residue 63 to 70 (63SKNGQVSP70 vs. 63SGPNRQVLP70) (A1 in Fig. 3​3).). The N terminus of aCdtA is disordered up to residue 70 (i.e., residues 53–70 are disordered), indicating that these residues are not strongly associated with the main body.
Cross-references: PDB:2F2F
Protein: DP01012 (UniProt P27392)
Region: residues 57	to 93
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is no electron density for residues 57–93, indicating that
this portion (denoted loop 57–93 ) does not obey icosahedral symmetry.
Cross-references: PDB:1W8X
Protein: DP01012 (UniProt P27392)
Region: residues 57	to 93
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The bulk of the capsid is cemented together by protein P30, and the vertex is stabilized by the integral membrane protein P16. The latter seems to act as a metastable sensor, linking the symmetry-mismatched vertex base and receptor-binding spike shaft with the membrane and providing a mechanism for the 
controlled extrusion of a membrane–protein–DNA tube to initiate host entry
analysis
Protein: DP01012 (UniProt P27392)
Region: residues 57	to 93
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The disordered loop 57–93 probably forms non-icosahedrally symmetric interactions with the vertex base, presumably explaining arms of electron density seen connecting the P16 region and capsid vertex in the cryo-EM.
Protein: DP01013 (UniProt P68927)
Region: residues 51	to 72
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues 51–72, which were not
resolved in the k Xis, do not show any regular structure in
HK022 Xis and thus appear to be completely disordered in
solution.
The residues from Asp51 to Ser72 are not included in any
regular structure element in HK022 Xis, as indicated by the
lack of any medium- or long-range NOEs. Hence, the
C terminus is largely disordered and displays very high local
RMSD values.
Cross-references: PDB:1PM6
Protein: DP01013 (UniProt P68927)
Region: residues 53	to 72
Annotation: protein binding (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
This finding shows
that
the
C-
terminal
region
of
Xis
is
required
for
Xis
-Int
DNA
binding
cooperativity.
The
observation
that
these
mutants
are
deficient
in
excisive
recombination
in
vivo
indicates
that
this
cooperativity
is
important
for
excision.
Protein: DP01013 (UniProt P68927)
Region: residues 53	to 72
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Taken
together,
these
results
provide
the
first
evidence
that
Xis-Int
cooperativity
probably
takes
place
through
direct
protein
-protein
interactions
between
Int
and
the
C-terminal
region
of
Xis,
and
not
through
Xis-induced
alterations
in
DNA
structure
that
in
turn
promote
Int
binding.
The
properties
of
the
mutant
Xis
(Xis-54)
lacking
the
C-terminal
19
amino
acids
in
the
excision,
challenge
phage
and
gel
retardation
assays
demonstrate
that
the
N-terminal
53
amino
acids
of
Xis
are
sufficient
to
promote
X
excision,
bind
the
DNA
and
interact
cooperatively
with
FIS.
Protein: DP01014 (UniProt O94742)
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:
Curator statement: This entry corresponds to the bound state of Sem1 to Sac3 and Thp1. The crystal structure shows that Sem1 interacts in a mostly extended conformation, with the exception of the C-terminal helix. Several amino acids from the N-terminus and the central region do not possess electron density. 
No electron density was observed for the poorly-conserved residues (1-22) at the Sem1 N-terminus, and between the N and C-terminal binding sites (residues 42-52).
Cross-references: PDB:3T5V
Protein: DP01014 (UniProt O94742)
Region: residues 1	to 70
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Sem1 residues 23-41 bind in a positively charged cleft formed by the TPR-like helices of the Thp1 superhelical domain (Fig. 2c,d). In this cleft, aspartates and glutamates from Sem1 form extensive ionic interactions and hydrogen bonds with several Thp1 helices (Fig 2c).
A single Sem1 chain wraps intimately around Thp1, but makes little contact with Sac3, demonstrating that Sem1 is a stoichiometric component of the TREX-2 complex. Sem1 makes extensive contacts with Thp1, burying 2741 Å2 of surface area, but makes only minor contact to Sac3, burying 293 Å2 (Supplementary Movie 2). Sem1 residues 53-89 make extensive interactions across the surface of the Thp1 superhelical domain and form a strongly conserved C-terminal helix (Supplementary Fig. 1) that binds in the cleft formed between helices α16 and α17 of the winged helix domain (Fig. 2a,b).
Cross-references: PDB:3T5V
Protein: DP01014 (UniProt O94742)
Region: residues 1	to 70
Annotation: protein folding chaperone (Molecular function)
Evidence: heterologous protein expression evidence used in manual assertion
Supporting statements:
When expressed alone, Thp1 remained insoluble irrespective of the use of a range of solubilizing tags (Fig. 1a, lane 1), but its solubility improved dramatically when coexpressed with Sem1 (Fig. 1a, lane 2).Furthermore, Sem1 was not pulled down by Sac3 unless Thp1 was present (Fig. 1a, lanes 4 and 5), indicating that Sem1 stabilizes Thp1 and in turn facilitates formation of a stoichiometric Sac3–Thp1–Sem1 complex in vitro.
Although Sem1 has been proposed to function as the “molecular glue” that holds Sac3 and Thp1 together32, in TREX-2 Sem1 makes few contacts with Sac3 and instead appears to facilitate complex formation by stabilizing Thp1.
Cross-references: PDB:3T5V
Protein: DP01014 (UniProt O94742)
Region: residues 1	to 70
Annotation: molecular adaptor activity (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Yeast expressing sem1-Δ5link displayed levels of proteasomes and lid subcomplexes equivalent to cells expressing WT SEM1, and they incorporated Rpn3 into the lid and LP3 (Figure 5B). However, yeast expressing sem1-Δ11link or sem1-Δ15link had decreased levels of proteasomes compared to yeast with WT SEM1, and they did not accumulate detectable levels of LP3. Yeast expressing sem1-Δ19link were severely depleted for 26S proteasomes and free lid and had no detectable LP3 (Figure 5B)”.
The variability of the linker sequence, together with the requirement for a minimal length for efficient LP3 assembly, lead us to conclude that the linker functions primarily as a flexible spacer between Sem1 site 1 and site 2 that permits their optimal binding to Rpn3 and Rpn7
The two conserved acidic sites at opposing ends of a poorly conserved linker sequence allow Sem1 to tether Rpn3 and Rpn7 to one another until their interface can be reinforced or remodeled via docking to other lid subunits”, “Rpn3-Rpn7 tethering by Sem1 requires physical linkage between Sem1 site 1 and site 2, and the linker must be ≥10 residues in length to function normally in proteasome biogenesis (Figure 4A)
Cross-references: PDB:3T5V
Protein: DP01014 (UniProt O94742)
Region: residues 1	to 70
Annotation: protein binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Human Rpn3 contacts Sem1 site 1 (Wei et al., 2008). The site of interaction between Rpn7 and Sem1 is poorly defined, although EM analysis suggests that Rpn7 binds the C-terminal region of Sem1 (Bohn et al., 2013). We confirmed that mutation of the eight residues of site 1 (Figure 1A) to alanines disrupted Sem1 interaction with yeast Rpn3 (Figure 3A, left panel); in contrast, this had no effect on binding to Rpn7 (Figure 3A, right panel). Conversely, mutation of the absolutely conserved Trp60 and Trp64 residues in Site 2 disrupted Sem1 binding to Rpn7 while leaving binding to Rpn3 intact (Figure 3A). These data indicate that Sem1 site 1 and site 2 contribute to independent binding sites for Rpn3 and Rpn7.
The authors use a set of Rpn3, Rpn7 and Sem1 mutants, expressed in yeast, and tag-based purifications of the macro-complex to decipher the role of Sem1 in the formation of the proteosomal lid. They demonstrate that two separate motifs, enriched in charged residues, are responsible of the interaction. As well, the length of the linker also determines the efficient tethering effect of Sem1.