LiteFold/DisProt huggingface dataset:
Protein: DP03040 (UniProt A8ULG6)
Region: residues 162	to 175
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 162 to 175 were disordered and therefore not included in the final model.
Cross-references: PDB:4I0N
Protein: DP03042 (UniProt Q9UBU7)
Region: residues 255	to 293
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Thirty-seven residues belonging to the linker that connects the coil region of DBF4 motif M to β3 of the Zn2+ binding domain of motif C are disordered in the crystals.
Cross-references: PDB:4F9A
PDB:4F9C
PDB:4F99
PDB:4F9B
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 19	to 74
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The results of structural calculation revealed that the
N-terminal residues 9–18 form an a-helix (N-helix), as
predicted previously (Stutz et al. 2000). The helical structure is supported by the chemical shift index (Wishart and
Sykes 1994), strong sequential HN-HN NOE contacts, and
several weak NOEs between residue side chains (Fig. 3A,B). One side of the N-helix is formed by hydrophobic residues,
and the opposite side is polar. The N-helix is likely to be
transient, as the values of heteronuclear 15N[1
H] NOEs for
this region were significantly reduced compared with those
for the RRM (Fig. 6B, see below), and the intensities of Ha/
Hb(i) to HN(i+3/i+4) NOE cross-peaks were smaller than
expected for stable a-helices. The remainder of the N domain appears largely unstructured, although some regions
have restricted mobility (see below).
The absence of long-range proton–proton NOEs and
reduced 15N[1
H] NOEs indicates that the N domain is
flexible (Fig. 6B, see below) yet has restricted mobility in
the following regions: amino acids 6–23, 30–34, and 46–62,
mapping to the N-helix, and Arg- and aromatic-rich
regions, respectively (Fig. 1). This suggests that regions of
the N domain may have the propensity to form local structure and/or interact with other parts of REF2-I.
Cross-references: PDB:2F3J
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 19	to 58
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The RNA binding activity of NM was investigated here
using NMR chemical shift and dynamic mapping. In 50 mM
L-Arg, L-Glu a number of residues from the N domain of
NM displayed signal shifts on addition of a 15-mer RNA
oligonucleotide (Fig. 6A, left panel, B) with changes for
amino acids 7–24 and 29–47 being most pronounced, consistent with EMSA data (Rodrigues et al. 2001; Zenklusen et al. 2001.)
To investigate further which residues participate in RNA
binding we measured the changes in heteronuclear 15N[1
H]
NOEs that provide a quantitative parameter for mobility of
polypeptide chain. Residues 15–58 show significantly increased heteronuclear 15N[1
H] NOEs upon addition of
RNA, indicating reduced mobility and direct involvement
in RNA binding (Fig. 6B), even in high-salt buffer, yet the
heteronuclear 15N[1
H] NOEs for amino acids 7–14 were
virtually unchanged, implying these residues are not directly involved in RNA binding, despite the changes in their
amide signal positions.
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 29	to 41
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We investigated
the changes in the HSQC spectra on
addition of nonlabeled DDX39 to
15N,2
H-labeled NM. A significant number of NM signals in the NM:DDX39
disappear from the spectra due to line
broadening, suggesting that both the
N and RRM domains are involved in
complex formation (Fig. 8A,C).
In the N
domain, signals disappear within amino acids 5–16, which
includes a major part of the N-helix, and additionally within
amino acids 29–41 from the Arg-rich region. Together the
biochemical and NMR data indicate that NM presents an
extended binding interface for DDX39 involving both the N
and RRM domains.
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 23	to 48
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of HSQC spectra of 15N,2
H-NM upon addition
of TAP-p15 revealed that signals from amino acids 8, 9, 17
(N-helix), and 23–48 (Arg-rich) of the N domain are broadened and disappear from the spectra (Fig. 8B,C). In
contrast to the complex of NM with DDX39, no signals
belonging to the RRM disappear completely nor are shifted
significantly in the NM:TAP-p15 spectra.
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 19	to 53
Annotation: protein binding (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
We assessed the contribution of the N and RRM domains to the DDX39 interaction using GST pull-down assays (Fig. 8D). The
D53 construct was used in these assays, since further
truncation of the protein leads to extensive perturbation of the HSQC spectrum for the RRM (Fig. 4C).
Whereas NM showed a strong interaction with DDX39, the D53 construct encompassing the RRM showed a weak
interaction.
This is consistent with the GST pull-down data,
which show that TAP interacts weakly with the RRM and
more strongly with NM (Fig. 8D).
Protein: DP03043 (UniProt Q9JJW6)
Region: residues 24	to 48
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR experiments therefore all indicate that ALYREF
partially displaces the viral RNA initially bound specifically to
ORF57, but retains it within the complex. In the ternary complex
ORF57 aa106–120 directly interacts with the ALYREF RRM,
whereas flexible flanking regions of ALYREF (aa24–48) and
ORF57 (aa81–92), and to lesser extent, parts of helix 2 of the
ALYREF RRM, jointly keep hold of the viral RNA molecule.
Interestingly, amide signals from flexible protein regions which
become involved in direct contacts with RNA (as evidenced by
RNA-protein saturation transfer), are only partially broadened in
the complex. They had intensities higher than signals from the
folded regions, but lower than signals from the unfolded noninteracting regions (examples of this behavior can be seen in Fig. 5
and Fig. S5). This suggests that the interaction with RNA in these
conditions was somewhat transient and did not lead to the
formation of a rigid 3D structure.
Protein: DP03044 (UniProt Q9UIF9)
Region: residues 496	to 519
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The
13C secondary chemical shifts, 15N relaxation rates and
low {1H}-
15N heteronuclear NOE values for the amides of
residues 496–519 and 622–664 (comprising the AT-hooks)
indicate that these regions are flexible and intrinsically disordered, while residues 520–621 are structured and define
the globular fold of the TAM domain.
Protein: DP03044 (UniProt Q9UIF9)
Region: residues 622	to 664
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 The
13C secondary chemical shifts, 15N relaxation rates and
low {1H}-
15N heteronuclear NOE values for the amides of
residues 496–519 and 622–664 (comprising the AT-hooks)
indicate that these regions are flexible and intrinsically disordered, while residues 520–621 are structured and define
the globular fold of the TAM domain.
Protein: DP03044 (UniProt Q9UIF9)
Region: residues 1731	to 1797
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
Our attempts at crystallizing constructs harboring both reader domains have failed to date. Likely the unstructured nature of the linker amino acid sequence between the PHD finger and the BRD prevented our efforts in crystallizing the full-length tandem proteins.
The supplementary figure S1 shows this region is disordered.
Protein: DP03045 (UniProt P30429-2)
Region: residues 1	to 105
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CED-4b exhibits a similar structure, except that its CARD domain is flexible and disordered in the crystals.
However, the CARD domain of CED-4a adopts a rigid conformation through interactions with thea/b-fold of CED-4b and CED-9, whereas the CARD domain of CED-4b is disordered in the crystals.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 1	to 160
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of
the ICP27 N-terminal 160 amino acids (Fig. 5A) were consistent with a protein in a random-coil conformation due to the
shape of the CD curve (31).
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 1	to 160
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
1
H-15N HSQC spectra
for the ICP27 N-terminal protein alone showed peaks that
were not well dispersed in the proton dimension and that
resonated between 7.5 and 9.0 ppm (Fig. 5B). Proton HSQC
chemical shifts in this range are typical of shifts found in
proteins with a random-coil conformation (42). Each HSQC
signal represents one N-H group in the protein, and there
should be at least 1 peak per amino acid of the protein. Approximately 70 clearly defined HSQC peaks were observed in
the ICP27 N-terminal HSQC spectra, which is less than half of
the expected 160 HSQC peaks. There was also a high degree of
signal overlap in the region between 8.0 and 9.0 ppm in the
proton dimension and in the region between 120 and 124 ppm
in the nitrogen dimension, which prevents the resolution of all
160 HSQC peaks. The lack of peak dispersion and the high
degree of peak overlap in the ICP27 N-terminal HSQC spectrum suggests that the protein is not in a single conformation,
nor is it rigidly folded.
HET-NOE spectrum of the ICP27 N-terminal 160 amino
acids reveals a flexible yet compact conformation.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 150
Annotation: nucleic acid binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
The gC oligonucleotide
gC 1-30 was shifted well by the wild-type ICP27 N-terminal
protein (Fig. 1B). The substitution of lysine for arginine at
residue 148 (R148K) or at residues 138 and 150 (R138,150K)
did not affect the ability of the ICP27 N terminus to shift the
gC 1-30 sequence. An arginine-to-lysine substitution at residue
138 or 150 also did not affect the ability of the ICP27 N
terminus to shift gC 1-30 (data not shown). However, triple
arginine-to-lysine substitutions at residues 138, 148, and 150
showed reduced binding because the mutant protein did not
efficiently shift gC 1-30. 
The R138,148,150K mutant binds poorly to GC-rich sequences bound by wild-type (WT) ICP27.
These results suggest that three arginines at
positions 138, 148, and 150 within the RGG box motif are all
required to efficiently shift gC sequences.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 150
Annotation: nucleic acid binding (Molecular function)
Evidence: co-localization evidence used in manual assertion
Supporting statements:
To determine if arginine residues 138, 148,
and 150 within the RGG box were also required for efficient
RNA export by ICP27 during infection, we looked at the localization of poly(A) RNA at 8 h after infection, when viral
transcription is much more active than cellular transcription
(40). Cells were infected with wild-type HSV-1 KOS and the
RGG, R138,150K, and R138,148,150K mutants (Fig. 2).
Poly(A) was visualized by hybridization with an oligo(dT)
probe. ICP27 is actively shuttling at 8 h after infection and was
seen to be predominantly cytoplasmic in both wild-type and
mutant infections (Fig. 2). Poly(A) was seen to be distributed
in the cytoplasm of KOS-infected cells, as expected, whereas
poly(A) RNA was confined to the nucleus in RGG-infected
cells, as seen previously. Poly(A) RNA was seen to be present
in the cytoplasm of cells infected with the R138,150K mutant,
but in contrast, poly(A) RNA was nuclear in cells infected
with the R138,148,150K mutant (Fig. 2).
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 150
Annotation: protein export from nucleus (Biological process)
Evidence: co-localization evidence used in manual assertion
Supporting statements:
To determine if arginine residues 138, 148,
and 150 within the RGG box were also required for efficient
RNA export by ICP27 during infection, we looked at the localization of poly(A) RNA at 8 h after infection, when viral
transcription is much more active than cellular transcription
(40). Cells were infected with wild-type HSV-1 KOS and the
RGG, R138,150K, and R138,148,150K mutants (Fig. 2).
Poly(A) was visualized by hybridization with an oligo(dT)
probe. ICP27 is actively shuttling at 8 h after infection and was
seen to be predominantly cytoplasmic in both wild-type and
mutant infections (Fig. 2). Poly(A) was seen to be distributed
in the cytoplasm of KOS-infected cells, as expected, whereas
poly(A) RNA was confined to the nucleus in RGG-infected
cells, as seen previously. Poly(A) RNA was seen to be present
in the cytoplasm of cells infected with the R138,150K mutant,
but in contrast, poly(A) RNA was nuclear in cells infected
with the R138,148,150K mutant (Fig. 2).
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 136	to 140
Annotation: methylation display site (Disorder function)
Evidence: in vivo methylation assay evidence used in manual assertion
Supporting statements:
This annotation refers to the mathylation of the Arg 138 residue of ICP27 protein.
The arginines at positions 138, 148, and 150 were consistently found to be methylated in these experiments.
The arginine at position 138 was found to be dimethylated in the cytoplasmic fraction.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 147	to 151
Annotation: methylation display site (Disorder function)
Evidence: in vivo methylation assay evidence used in manual assertion
Supporting statements:
This annotation refers to the mathylation of Arg 148  and Arg 150 residues of ICP27 protein.
The arginines at positions 138, 148, and 150 were consistently found to be methylated in these experiments.
In the data analysis shown in Fig.2B, the arginine at position 148 was found to be monomethylated and the arginine at position 150 was found to be dimethylated in the nuclear sample in this experiment.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 151
Annotation: negative regulation of viral genome replication (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
DNA replication was also reduced relative to that for wild-type KOS, in that viral DNA copies per cell were found to be about 2.5 to 5 times lower for the mutants, as measured by quantitative real-time PCR of the glycoprotein C (gC) locus (Fig. 6B).
DNA copy number was reduced in the presence of this drug, but not to the extent seen with the arginine substitution mutants. This does suggest, however, that the arginine substitution mutants are impaired because of hypomethylation.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 151
Annotation: regulation of protein stability (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
ICP27 arginine-to-lysine mutant proteins are less stable than wild-type (WT) HSV-1 ICP27. HeLa cells were infected with WT HSV-1 KOS, ΔRGG, or the indicated ICP27 arginine-to-lysine viral mutants.
Hypomethylation of ICP27 had two major effects, decreased protein stability ​(Fig.7) and an earlier and more rapid export of ICP27 from the nucleus to the cytoplasm (Fig.11). The same effects were observed with the methylase inhibitor AdOx. These results strongly suggest that it is the hypomethylation of ICP27, rather than structural changes that may have occurred in the RGG box associated with mutating arginines to lysines, that is responsible for the reduced stability and more-rapid nuclear export of ICP27.
The amminoacids sequence reported (138-151) contains three substitutions arginine to lysine at position 138, 148 and 150.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 138	to 151
Annotation: negative regulation of viral transcription (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Global transcription of the ICP27 arginine-to-lysine viral mutants is decreased.
Moderate decreases in the levels of all classes of viral transcripts were seen for the three single mutants (Fig. 5, left panels), and more notable decreases in some early and late transcript levels were seen for the double and triple mutants (Fig. 5, right panels).
The amminoacids sequence reported (138-151) contains three substitutions arginine to lysine at position 138, 148 and 150.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 136	to 140
Annotation: methylation display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
This annotation refers to the methylation of the Arg 138 residue of the ICP27 protein.
The single substitutions R138K and R148K had relatively little effect on ICP27 methylation, while R150K produced about a twofold reduction (Fig. 3). However, the R138,150K double mutant and the R138,148,150K triple mutant showed a substantial reduction in methylation. Methylation of the d4-5 mutant (ΔRGG) was not detectable, as we saw previously.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 147	to 151
Annotation: methylation display site (Disorder function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
This annotation refers to the methylation of the Arg 148 and Arg 150 residues of the ICP27 protein.
The single substitutions R138K and R148K had relatively little effect on ICP27 methylation, while R150K produced about a twofold reduction (Fig. 3). However, the R138,150K double mutant and the R138,148,150K triple mutant showed a substantial reduction in methylation. Methylation of the d4-5 mutant (ΔRGG) was not detectable, as we saw previously.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 72	to 76
Annotation: methylation display site (Disorder function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
Other arginines scattered throughout the protein were also found to be methylated, but these residues were not located at the major site of methylation, the RGG box (Fig. 1B and C).
Supplementary data shows residues R74, R111 and R119, within the IDR were found to be methylated.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 109	to 113
Annotation: methylation display site (Disorder function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
Other arginines scattered throughout the protein were also found to be methylated, but these residues were not located at the major site of methylation, the RGG box (Fig. 1B and C).
Supplementary data shows residues R74, R111 and R119, within the IDR were found to be methylated.
Protein: DP03046 (UniProt Q9J0X9)
Region: residues 117	to 121
Annotation: methylation display site (Disorder function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
Other arginines scattered throughout the protein were also found to be methylated, but these residues were not located at the major site of methylation, the RGG box (Fig. 1B and C).
Supplementary data shows residues R74, R111 and R119, within the IDR were found to be methylated.
Protein: DP03047 (UniProt O62301)
Region: residues 194	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loops are highlighted with dotted lines.
Cross-references: PDB:5NKK
PDB:5NKM
Protein: DP03047 (UniProt O62301)
Region: residues 255	to 288
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered loops are highlighted with dotted lines.
Cross-references: PDB:5NKM
PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 124	to 133
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The GDP moiety bound to the SMG9 G domain is shown in stick representation. Disordered loops are highlighted with dotted lines.
Cross-references: PDB:5NKM
PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 153	to 171
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
First, there is a conserved proline residue (Pro153SMG9, disordered in the present structure) at the position of switch 2 typically occupied by a glycine (Fig. 2B,C).
Cross-references: PDB:5NKM
PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 285	to 307
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
At the corresponding position of Asp218Atlastin, SMG9 features a conserved lysine residue (Lys241SMG9) that stacks with its aliphatic portion on top of the guanine base. With the caveat that motif  G5 is largely  disordered, none of the interactions in the current structure engage guanine-specific moieties. 
Cross-references: PDB:5NKM
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 124	to 133
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The G domains of SMG8c and SMG9c face each other and interact with part of their convex surfaces (Fig. 1B).
Cross-references: PDB:5NKM
PDB:5NKK
Protein: DP03048 (UniProt Q9XWJ1)
Region: residues 107	to 139
Annotation: molecular sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
GDP binds SMG9c at a similar position as in Atlastin and GBP1, in particular with similarities at the phosphatebinding loops, e.g., at the motifs G1 (P loop), G2 (switch 1), and G3 (switch 2) (Fig. 2B,C). In SMG9c, the P loop residues Lys99SMG9 and Ser100SMG9 coordinate the phosphates of GDP. Although parts of the switch regions are disordered in our GDP-bound structure, the switch 2 residue Asp150SMG9 is at the position expected for coordinating the magnesium ion, while the switch 1 residue Thr135SMG9 is 10 Å away from the position expected upon γ -phosphate binding.
Cross-references: PDB:5NKK