LiteFold/DisProt huggingface dataset:
Protein: DP03058 (UniProt Q58F21)
Region: residues 209	to 220
Annotation: localization (Biological process)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
We identified a 12-amino acid stretch (KGVKRKADTTTP) in the inter-bromodomain region that is perfectly conserved among the BET family of proteins (Fig. 1). To investigate the function of this motif, we deleted the 12 residues and expressed the mutant proteins tagged with GFP in HEK293T cells.
In humans, the BET family consists of four members, BRD2, BRD3, BRD4 and BRDT, that all normally localize to the nucleus. We identified a 12-amino acid stretch in the inter-bromodomain region that is perfectly conserved among the BET family members. We deleted these residues and expressed the mutant proteins in HEK293T cells to investigate the function of this motif. We found that the deletion of this motif alters the localization of BET proteins.
Nevertheless, BET mutants lacking the reported nuclear localization signal motif but re-taining the 12-amino acid stretch resided in the nucleus. Furthermore, these mutants were diffused throughout the cytoplasm when the 12 residues were removed. These results indicate that the conserved amino acid stretch in the inter-bromodomain region of the BET family functions as a nuclear localization signal
In summary, we conclude that the conserved 12-amino acid sequence in the inter-bromodomain is at least part of the nuclear localization signal and plays important roles in the cytoplasmic/nuclear partitioning of the BET proteins.
Protein: DP03058 (UniProt Q58F21)
Region: residues 209	to 220
Annotation: localization (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
We identified a 12-amino acid stretch (KGVKRKADTTTP) in the inter-bromodomain region that is perfectly conserved among the BET family of proteins (Fig. 1). To investigate the function of this motif, we deleted the 12 residues and expressed the mutant proteins tagged with GFP in HEK293T cells.
In humans, the BET family consists of four members, BRD2, BRD3, BRD4 and BRDT, that all normally localize to the nucleus. We identified a 12-amino acid stretch in the inter-bromodomain region that is perfectly conserved among the BET family members. We deleted these residues and expressed the mutant proteins in HEK293T cells to investigate the function of this motif. We found that the deletion of this motif alters the localization of BET proteins.
Nevertheless, BET mutants lacking the reported nuclear localization signal motif but re-taining the 12-amino acid stretch resided in the nucleus. Furthermore, these mutants were diffused throughout the cytoplasm when the 12 residues were removed. These results indicate that the conserved amino acid stretch in the inter-bromodomain region of the BET family functions as a nuclear localization signal
In summary, we conclude that the conserved 12-amino acid sequence in the inter-bromodomain is at least part of the nuclear localization signal and plays important roles in the cytoplasmic/nuclear partitioning of the BET proteins.
Protein: DP03058 (UniProt Q58F21)
Region: residues 583	to 947
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
BRDT has a long C-terminal, largely unstructured extension of more than 300 residues after the ET domain, which might play a specific role in the function of this paralog.
Protein: DP03059 (UniProt Q15059)
Region: residues 429	to 556
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Most of BRD3-L outside of the core ET domain appears to be disordered.
15N HSQC spectra of BRD3-L and
BRD3-ET are shown in Fig. 3A. The majority of peaks in the
spectrum of BRD3-L (Fig. 3A, black) appear as intense, overlapping signals with amide proton shifts in the 8.0– 8.6 ppm region
of the spectrum, a pattern characteristic of the disordered polypeptide. A number of weaker and more dispersed signals are
also observed. In contrast, peaks in the 15N HSQC of BRD3-ET
(Fig. 3A, red) are well-dispersed, as expected of a small, folded
protein domain. An overlay of the two 15N HSQC spectra
reveals that almost all signals in the BRD3-ET spectrum are
essentially unchanged in the BRD3-L spectrum, indicating that
the folded ET domain takes up the same conformation in the
context of the longer polypeptide.
Protein: DP03059 (UniProt Q15059)
Region: residues 645	to 726
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Most of BRD3-L outside of the core ET domain appears to be disordered.
15N HSQC spectra of BRD3-L and
BRD3-ET are shown in Fig. 3A. The majority of peaks in the
spectrum of BRD3-L (Fig. 3A, black) appear as intense, overlapping signals with amide proton shifts in the 8.0– 8.6 ppm region
of the spectrum, a pattern characteristic of the disordered polypeptide. A number of weaker and more dispersed signals are
also observed. In contrast, peaks in the 15N HSQC of BRD3-ET
(Fig. 3A, red) are well-dispersed, as expected of a small, folded
protein domain. An overlay of the two 15N HSQC spectra
reveals that almost all signals in the BRD3-ET spectrum are
essentially unchanged in the BRD3-L spectrum, indicating that
the folded ET domain takes up the same conformation in the
context of the longer polypeptide.
Protein: DP03060 (UniProt P60340)
Region: residues 124	to 152
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
  The overall fold of the apo
structure is similar to that of the E. coli TruB–RNA complex (14)
but with one striking difference: a 29-aa segment (residues 124–152) of the apoprotein corresponding to the thumb-loop
region is disordered in the crystals and was not observed in the
electron density map.
A 29-amino acid segment containing residues
124–152 was not observed in the electron density.
 The most prominent
change is that a 29-aa segment (residues 124–152) of the protein
corresponding to the thumb-loop region, which is totally disordered in the apoprotein, becomes ordered on RNA binding. It
is possible that the thumb loop is unstructured in the RNA-free
state, or it oscillates between free and bound forms, and the
RNA binding shifts the equilibrium to the bound form.
Cross-references: PDB:1R3F
Protein: DP03061 (UniProt P54132)
Region: residues 1093	to 1106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of the second molecule (Mol-B), which is illustrated in Figure 3b, is essentially the same except that the looping-out region (referred to as the BLM-insertion) is disordered.
Structure of Mol-A. Secondary-structure elements (five α-helices and two β-strands) are labeled. The BLM-insertion (a.a. 1093–1106) and C-term extended loop (a.a. 1183–1194) are colored red
Cross-references: PDB:3WE2
PDB:3WE3
Protein: DP03061 (UniProt P54132)
Region: residues 1091	to 1110
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The long and flexible loop between α1 and α2 (α1–α2 loop, from H1091 to T1100), which has several missed N–H peaks in the 1H–15N HSQC (R1098, N1099, S1106 and G1107), is not well converged.
According to Fig2, PDB and UniProt sequence data, T1100 referred in the text has wrong numbering. The correct end boundary is the disordered regions is T1110.
Cross-references: PDB:2MH9
Protein: DP03061 (UniProt P54132)
Region: residues 1004	to 1014
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All of the residues of BLM are present in the final model with the exception of the first three residues at the N-terminus and eight at the C-terminus, and two loops spanning residues 1004–1016 and 1093–1106 which are disordered.
Cross-references: PDB:4CDG
Protein: DP03061 (UniProt P54132)
Region: residues 1092	to 1107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All of the residues of BLM are present in the final model with the exception of the first three residues at the N-terminus and eight at the C-terminus, and two loops spanning residues 1004–1016 and 1093–1106 which are disordered.
Cross-references: PDB:4CDG
PDB:4CGZ
Protein: DP03061 (UniProt P54132)
Region: residues 1195	to 1207
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the full-length protein, the C-term extended loop is followed by the 13 amino acids 1195SSSVKKQKALVAK1207, which tether the C-terminal HRDC domain (Figure 5d). Interestingly, this linker is considerably shorter than that of WRN (77 residues)
Missing atomic coordinates in the corresponding PDB files
Cross-references: PDB:3WE2
PDB:3WE3
Protein: DP03061 (UniProt P54132)
Region: residues 1195	to 1207
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the full-length protein, the C-term extended loop is followed by the 13 amino acids 1195SSSVKKQKALVAK1207, which tether the C-terminal HRDC domain (Figure 5d). Interestingly, this linker is considerably shorter than that of WRN (77 residues)
Cross-references: PDB:3WE2
PDB:3WE3
Protein: DP03062 (UniProt P40692)
Region: residues 86	to 97
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Accordingly, residues 86–97 have been omitted from our model owing to a lack of interpretable electron density.
The crystallographic model included amino-acid residues 3–85, 98–299 and 320–336. Atoms with little or no electron density were deemed to be disordered and were omitted from the final model.
Cross-references: PDB:4P7A
Protein: DP03062 (UniProt P40692)
Region: residues 301	to 319
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 301–320 in the hLN40 QTK loop are disordered; however, we can infer from MutL structures (Ban et al., 1999 ▸) that Lys311 within the PTK motif should act as the conserved basic, γ-phosphate-sensing residue
The crystallographic model included amino-acid residues 3–85, 98–299 and 320–336. Atoms with little or no electron density were deemed to be disordered and were omitted from the final model.
Cross-references: PDB:4P7A
Protein: DP03063 (UniProt Q9BRZ2)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the linker residues between TRIM56 and SopA, as well as the 17 N-terminal residues of TRIM56 were disordered and could not be observed in the electron density.
Cross-references: PDB:5JW7
Protein: DP03065 (UniProt P51400)
Region: residues 148	to 230
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The comparison between the [1
H,15N]-TROSY spectrum of a deuterated GB1-dsRBM12 and the [1
H,15N]-HSQC spectra
of both isolated dsRBM1 and dsRBM2 (Figure S1; see
the Supplemental Data available with this article online)
shows that the dsRBM resonances are identical in both
contexts, except for a few N- and C-terminal residues.
In addition, this comparison indicates that the interdomain linker is flexible, as the chemical shifts of the
linker residues have random coil values (Stefl et al.,
2005b).
Protein: DP03065 (UniProt P51400)
Region: residues 148	to 230
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These results indicate that the ADAR2
dsRBMs are independent domains separated by a flexible linker,similar to the two dsRBMs of PKR(Nanduriet al.,
1998).
Protein: DP03065 (UniProt P51400)
Region: residues 152	to 232
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This strategy could be used considering (1) the distinct RNA binding location for each dsRBMs, with no mutual interactions (Stefl et al., 2006), (2) the flexible unstructured linker connecting dsRBM1 and dsRBM2 in the complex (Stefl et al., 2006) and (3) an overlap in the RNA sequence of the joint region of the subcomplexes (Figure 1).
Cross-references: PDB:2L3J
PDB:2L3C
Protein: DP03065 (UniProt P51400)
Region: residues 152	to 232
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This strategy could be used considering (1) the distinct RNA binding location for each dsRBMs, with no mutual interactions (Stefl et al., 2006), (2) the flexible unstructured linker connecting dsRBM1 and dsRBM2 in the complex (Stefl et al., 2006) and (3) an overlap in the RNA sequence of the joint region of the subcomplexes (Figure 1).
Cross-references: PDB:2L3J
PDB:2L3C
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Distinctive feature of the spectrum is a large negative peak at
200 nm, typical of IDPs. Further, the lack of a shoulder in the
range 210-230 nm indicates that the protein has practically no
secondary structural elements.
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Considering the molecular mass of Df31, the onedimensional 1
H NMR spectrum has unexpectedly sharp resonance lines. In addition, the lack of signal dispersion typical
of folded proteins suggests that Df31 is either unfolded or may
have very little stable 3D structure.
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: temperature-induced protein unfolding evidence used in manual assertion
Supporting statements:
As seen, Df31 resists
boiling, whereas BSA precipitates, underscoring the mostly
disordered character of Df31.
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Another indirect indication of disorder is proteolytic sensitivity, signaling accessibility of the polypeptide chain. To explore
this opportunity, we have tested the effect of wide-specificity proteases (subtilisin and proteinase NOVO) and also a narrowspecificity protease (trypsin) on Df31. As seen (Figure 3B), each
enzyme digested Df31 within 5 min, even though the enzymes
were used at very low enzyme/substrate ratios, typically in the
order of 1:1000 to 1:2000 (w/w).
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In our case, on a Superdex 200 gel-filtration column, Df31
elutes at an apparent MW of about 67 kDa (Figure 7). This value
reflects the behavior of full-length native Df31, as confirmed by SDS-PAGE analysis of the protein eluting from the column.
On the SDS gel, the protein migrates as a single band with an
apparent MW of 31 kDa (data not shown), in accord with its
apparent MW reported originally.
Protein: DP03066 (UniProt O16043)
Region: residues 1	to 183
Annotation: disorder (Structural state)
Evidence: differential scanning calorimetry evidence used in manual assertion
Supporting statements:
As opposed
to this behavior, the calorimetric curve of Df31 is entirely flat,
showing no signs of a major cooperative structural transition.
Thus, Df31 lacks a folded structure; that is, it is disordered by
this criterion.
Protein: DP03067 (UniProt Q07475)
Region: residues 1	to 68
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
CD spectroscopy confirmed the lack of structure in the
isolated protein in solution (Fig. 1).
Protein: DP03068 (UniProt P24348)
Region: residues 1036	to 1047
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The activation loop (residues 1028 – 1048) in LET-23 is largely disordered with the  exception of the N-terminal fragment encompassing the DFG motif (residues 1028 – 1035).
Cross-references: PDB:5WNO
Protein: DP03068 (UniProt P24348)
Region: residues 1036	to 1047
Annotation: molecular function activator activity (Molecular function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
LET-23 has no such tyrosine phosphorylation site in its activation loop (Figure 3C), suggesting that the observed concentration-dependent increase in kinase activity likely arises  through the allosteric effects of intermolecular interactions within kinase oligomers  stabilized on the vesicle surfaces.
Protein: DP03068 (UniProt P24348)
Region: residues 1036	to 1047
Annotation: lipid binding (Molecular function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
Like human EGFR, LET-23 is also inactive in solution, but its activity is significantly increased by concentrating it on the surface of lipid vesicles - implicating the involvement of intermolecular interactions in kinase activation.
Figure 3. Catalytic activity of the LET-23 kinase domain in solution and associated with lipid  vesicles .
Protein: DP03069 (UniProt P34712)
Region: residues 666	to 715
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues of the N-terminus (1–3, 52–54), the linker region (666– 715) and the C-terminus (1307–1321) were not visible in the electron density map and were  not included in the final structure. 
Cross-references: PDB:4F4C
Protein: DP03069 (UniProt P34712)
Region: residues 1307	to 1321
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues of the N-terminus (1–3, 52–54), the linker region (666– 715) and the C-terminus (1307–1321) were not visible in the electron density map and were  not included in the final structure. 
Cross-references: PDB:4F4C
Protein: DP03069 (UniProt P34712)
Region: residues 666	to 715
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues of the N-terminus (1–3, 52–54), the linker region (666– 715) and the C-terminus (1307–1321) were not visible in the electron density map and were  not included in the final structure. 
This flexible linker connects nucleotide binding domain 1 (NBD1)  and transmembrane domain 2 (TMD) of protein P-gp.
Cross-references: PDB:4F4C
Protein: DP03070 (UniProt Q8TEQ6)
Region: residues 1297	to 1412
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All experimental conditions we assayed
yielded samples that provide NMR data in agreement with
the absence of tertiary structure (Supplementary Figure
S1). Only ∼80% of the signals corresponding to the RBS1 domain were defined in the spectrum, precluding the unambiguous assignment of all resonances. Still, we have assigned
some fragments of the sequence using standard backbone
triple resonance experiments. Based on these assignments
and on the dispersion of the NMR signals shown in the
spectrum, we conclude that the RBS1 construct has a short
helical conformation surrounded by unstructured regions,
yielding the ensemble of flexible conformations observed
in 2D and 3D NOESY (Nuclear Overhauser effect spectroscopy) experiments.
Protein: DP03070 (UniProt Q8TEQ6)
Region: residues 1297	to 1412
Annotation: RNA binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
Therefore,
we conclude that a bipartite RNA-binding site, comprising
residues 1297–1412 (RBS1) and 1383–1508 (RBS2), within
the C-terminal region of Gemin5 enables a direct interaction with the IRES element with RBS1 being more intense
than RBS2 in UV-crosslinking experiments.
Protein: DP03070 (UniProt Q8TEQ6)
Region: residues 1294	to 1361
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Interestingly, the protein RBS11361-HIS encompassing mostly the predicted unstructured region of RBS1 retained RNA-binding activity (Fig. 2C), although with moderate affinity relative to HIS-RBS11412 (Table 1). Similar results were observed with HIS-RBS11361 (Fig. 2D).
Protein: DP03071 (UniProt Q92499)
Region: residues 72	to 85
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein construct used in the final crystallization setup
consisted of residues 72–283 of human DDX1; however, clear
electron density was only observed for residues 86–275 of
chain A and residues 86–279 of chain B. The residues at the Nand C-terminus that could not be modelled are likely to be
disordered in the crystal since we observed some ambiguous
density that could not be interpreted.
Cross-references: PDB:4XW3
Protein: DP03072 (UniProt P53420)
Region: residues 1656	to 1671
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
SM3' was disordered and was not visible in either a2NC1 homo or a4NC1 homo (Fig. 3)
Cross-references: PDB:5NB1