LiteFold/DisProt huggingface dataset:
Protein: DP02170 (UniProt O15234)
Region: residues 137	to 283
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
MLN51-S corresponds to a short region of MLN51 (residues 137–283 of a total of 703 residues). We tested whether a similar complex can be assembled with the N-terminal half (TAP-MLN51-Nt, 1–351), the C-terminal half (TAP-MLN51-Ct, 352–703) or the full-length MLN51 protein (TAP-MLN51-FL, 1–703). We separately mixed TAP-MLN51-S, TAP-MLN51-Nt, TAP-MLN51-Ct and TAP-MLN51-FL with eIF4AIII and MAGOH-Y14ΔN in the presence of AMP-PNP and ssRNA as in our previous assays. TAP-MLN51-S, TAP-MLN51-Nt and TAP-MLN51-FL, which contain the SELOR domain, coprecipitated eIF4AIII and MAGOH-Y14ΔN with the same efficiency.
When TAP-MLN51-S was used as bait, neither eIF4AIII nor MAGOH-Y14ΔN were coprecipitated, indicating that MLN51-S does not stably interact with eIF4AIII or MAGOH-Y14ΔN individually (Fig. 1a, lanes 2 and 6).
Protein: DP02170 (UniProt O15234)
Region: residues 137	to 283
Annotation: single-stranded RNA binding (Molecular function)
Evidence: cross-linking evidence used in manual assertion
Supporting statements:
eIF4AIII and MLN51-S crosslinked to the RNA only in the presence of AMP-PNP, and no cross-linking was detected when the same mixture was not UV irradiated (Fig. 5, lanes 4–6). Thus, RNA cross-linking depends on complex assembly. This was confirmed by analyzing TAP-eIF4AIII and TAP-MLN51-S, as corresponding cross-links were shifted in the presence of the tag (Fig. 5, lanes 7–12). Therefore, both eIF4AIII and MLN51-S directly bind ssRNA in the complex.
Protein: DP02170 (UniProt O15234)
Region: residues 137	to 283
Annotation: regulation of RNA helicase activity (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
We measured eIF4AIII ATPase activity with or without its binding partners. TAP-tagged proteins purified successively on nickel and calmodulin affinity columns were used for this assay to reduce background NTPase activity originating from contaminating E. coli NTPases31. As expected, TAP-eIF4AIII had weak ATPase activity (Fig. 7b, top). Addition of an equimolar amount of TAP-MLN51-S increased this activity three-fold, correlating with the ability of MLN51-S to enhance binding of eIF4AIII to RNA.
Protein: DP02170 (UniProt O15234)
Region: residues 137	to 283
Annotation: nucleoplasm (Cellular component)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Confocal microscopic analysis indicated that MLN51-S WT was mainly restricted to the speckles' periphery (stained with antibodies raised against the splicing factor 9G8 in Fig. 8a–d).
Protein: DP02171 (UniProt P08621)
Region: residues 1	to 33
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The present model of the chymotrypsin-trimmed U1 snRNP (hereafter referred to as U1 snRNP) includes residues 1–164 of native U1 snRNA, a region covering the RRM and an N-terminal extension of the U1-70K protein (residues 34–183 out of 437 amino acids total), the N-terminal RRM of the U1-A protein (residues 1–114 out of 282 amino acids total) and the Sm folds with varying terminal appendices of all seven Sm proteins but lacks U1-C (see also Supplementary Figure S3 and Supplementary Table SI for protein residues included in the model).
In our structure, the electron density for the U1-70K N-terminal extension fades out beyond the centre of the Sm ring, indicating that the very N terminus of U1-70K is degraded or disordered.
Cross-references: PDB:3PGW
Protein: DP02171 (UniProt P08621)
Region: residues 1	to 33
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The present model of the chymotrypsin-trimmed U1 snRNP (hereafter referred to as U1 snRNP) includes residues 1–164 of native U1 snRNA, a region covering the RRM and an N-terminal extension of the U1-70K protein (residues 34–183 out of 437 amino acids total), the N-terminal RRM of the U1-A protein (residues 1–114 out of 282 amino acids total) and the Sm folds with varying terminal appendices of all seven Sm proteins but lacks U1-C (see also Supplementary Figure S3 and Supplementary Table SI for protein residues included in the model).
In our structure, the electron density for the U1-70K N-terminal extension fades out beyond the centre of the Sm ring, indicating that the very N terminus of U1-70K is degraded or disordered.
Protein: DP02171 (UniProt P08621)
Region: residues 184	to 437
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The present model of the chymotrypsin-trimmed U1 snRNP (hereafter referred to as U1 snRNP) includes residues 1–164 of native U1 snRNA, a region covering the RRM and an N-terminal extension of the U1-70K protein (residues 34–183 out of 437 amino acids total), the N-terminal RRM of the U1-A protein (residues 1–114 out of 282 amino acids total) and the Sm folds with varying terminal appendices of all seven Sm proteins but lacks U1-C (see also Supplementary Figure S3 and Supplementary Table SI for protein residues included in the model).
Protein: DP02171 (UniProt P08621)
Region: residues 184	to 437
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The present model of the chymotrypsin-trimmed U1 snRNP (hereafter referred to as U1 snRNP) includes residues 1–164 of native U1 snRNA, a region covering the RRM and an N-terminal extension of the U1-70K protein (residues 34–183 out of 437 amino acids total), the N-terminal RRM of the U1-A protein (residues 1–114 out of 282 amino acids total) and the Sm folds with varying terminal appendices of all seven Sm proteins but lacks U1-C (see also Supplementary Figure S3 and Supplementary Table SI for protein residues included in the model).
Analysis of washed crystals revealed that a C-terminal RS-like region of U1-70K, a C-terminal RNA recognition motif (RRM) of U1-A, the U1-C protein as well as a C-terminal RG-repeat/Pro-rich region of Sm protein B were removed during the crystallization, while the RNA remained intact (Supplementary Figure S1).
Cross-references: PDB:3PGW
Protein: DP02171 (UniProt P08621)
Region: residues 184	to 437
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The present model of the chymotrypsin-trimmed U1 snRNP (hereafter referred to as U1 snRNP) includes residues 1–164 of native U1 snRNA, a region covering the RRM and an N-terminal extension of the U1-70K protein (residues 34–183 out of 437 amino acids total), the N-terminal RRM of the U1-A protein (residues 1–114 out of 282 amino acids total) and the Sm folds with varying terminal appendices of all seven Sm proteins but lacks U1-C (see also Supplementary Figure S3 and Supplementary Table SI for protein residues included in the model).
Analysis of washed crystals revealed that a C-terminal RS-like region of U1-70K, a C-terminal RNA recognition motif (RRM) of U1-A, the U1-C protein as well as a C-terminal RG-repeat/Pro-rich region of Sm protein B were removed during the crystallization, while the RNA remained intact (Supplementary Figure S1).
For example, the alternative splicing factor ASF/SF2 binds to the RS-like domain of U1-70K (Xiao and Manley, 1997).
Cross-references: PDB:3PGW
Protein: DP02171 (UniProt P08621)
Region: residues 277	to 281
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We found that BAD1 was phosphorylated by SRPK1 in vitro, and the binding affinity of phosphorylated BAD1 to SRSF1, with a K d of 700nM, was 60‐fold weaker than that of the nonphosphorylated protein. Using mass spectrometry, we found that SRPK1 adds 8 to 9 phosphate groups on BAD1, and further identified the phosphorylation sites (Figure 4e). We identified seven unambiguous phosphorylation sites (Figure 4e). Two of three serine residues in the RSSRS motif (residues 291–295) were phosphorylated.
Figure 4 shows the phosphorylated serine residues are at position 245, 257, 259, 266, 268, 277, 281, and the serine residues in the RSSRS motif at 292, 293 and 295.
Protein: DP02171 (UniProt P08621)
Region: residues 265	to 269
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We found that BAD1 was phosphorylated by SRPK1 in vitro, and the binding affinity of phosphorylated BAD1 to SRSF1, with a K d of 700nM, was 60‐fold weaker than that of the nonphosphorylated protein. Using mass spectrometry, we found that SRPK1 adds 8 to 9 phosphate groups on BAD1, and further identified the phosphorylation sites (Figure 4e). We identified seven unambiguous phosphorylation sites (Figure 4e). Two of three serine residues in the RSSRS motif (residues 291–295) were phosphorylated.
Figure 4 shows the phosphorylated serine residues are at position 245, 257, 259, 266, 268, 277, 281, and the serine residues in the RSSRS motif at 292, 293 and 295.
Protein: DP02171 (UniProt P08621)
Region: residues 255	to 259
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We found that BAD1 was phosphorylated by SRPK1 in vitro, and the binding affinity of phosphorylated BAD1 to SRSF1, with a K d of 700nM, was 60‐fold weaker than that of the nonphosphorylated protein. Using mass spectrometry, we found that SRPK1 adds 8 to 9 phosphate groups on BAD1, and further identified the phosphorylation sites (Figure 4e). We identified seven unambiguous phosphorylation sites (Figure 4e). Two of three serine residues in the RSSRS motif (residues 291–295) were phosphorylated.
Figure 4 shows the phosphorylated serine residues are at position 245, 257, 259, 266, 268, 277, 281, and the serine residues in the RSSRS motif at 292, 293 and 295.
Protein: DP02171 (UniProt P08621)
Region: residues 243	to 247
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We found that BAD1 was phosphorylated by SRPK1 in vitro, and the binding affinity of phosphorylated BAD1 to SRSF1, with a K d of 700nM, was 60‐fold weaker than that of the nonphosphorylated protein. Using mass spectrometry, we found that SRPK1 adds 8 to 9 phosphate groups on BAD1, and further identified the phosphorylation sites (Figure 4e). We identified seven unambiguous phosphorylation sites (Figure 4e). Two of three serine residues in the RSSRS motif (residues 291–295) were phosphorylated.
Figure 4 shows the phosphorylated serine residues are at position 245, 257, 259, 266, 268, 277, 281, and the serine residues in the RSSRS motif at 292, 293 and 295.
Protein: DP02171 (UniProt P08621)
Region: residues 291	to 295
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We found that BAD1 was phosphorylated by SRPK1 in vitro, and the binding affinity of phosphorylated BAD1 to SRSF1, with a K d of 700nM, was 60‐fold weaker than that of the nonphosphorylated protein. Using mass spectrometry, we found that SRPK1 adds 8 to 9 phosphate groups on BAD1, and further identified the phosphorylation sites (Figure 4e). We identified seven unambiguous phosphorylation sites (Figure 4e). Two of three serine residues in the RSSRS motif (residues 291–295) were phosphorylated.
Figure 4 shows the phosphorylated serine residues are at position 245, 257, 259, 266, 268, 277, 281, and the serine residues in the RSSRS motif at 292, 293 and 295.
Protein: DP02171 (UniProt P08621)
Region: residues 230	to 306
Annotation: protein binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
In addition, BAD1 alone interacts with SRSF1 with a binding affinity comparable with full‐length U1‐70K, whereas BAD2 or RRM alone cannot.
Protein: DP02171 (UniProt P08621)
Region: residues 230	to 306
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To confirm our FP results and to eliminate possible interference of Arg/Glu in protein interaction, we further performed pull‐down assays in a buffer that has no Arg/Glu using purified His‐SUMO‐tagged U1‐70K constructs and phosphorylated SRSF1 obtained from E. coli (Figure 2). Our pull‐down assays confirmed the interaction between U1‐70K and SRSF1 (Figure 2), in consistent with FP assays shown in Figure 1.
Protein: DP02171 (UniProt P08621)
Region: residues 230	to 306
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Our circular dichroism (CD) spectra show that BAD1 contains both α‐helical structure and random coil, and hyper phosphorylated RS (pi‐RS) is mainly disordered (Figure 5a, dotted lines).
Protein: DP02173 (UniProt Q9BS26)
Region: residues 361	to 379
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-tail (residues 326–377) is flexible and mainly composed of random coils in addition to one short strand β16 (residues 369–370), which is antiparallel to β3 in domain a, and two short 310 helices: η4 (residues 326–328) and η5 (residues 358–360) filling the cavity lined by helices α7 and α9 in domain b′ (Fig 1A).
Cross-references: PDB:2R2J
Protein: DP02173 (UniProt Q9BS26)
Region: residues 361	to 406
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Moreover, the flexible C-tail (residues 351–372) becomes disordered with its electron density untraceable. The movements of the C-tail and the b′ domain disrupt the interactions among domains a, b′ and the C-tail, favoring an open conformation, thus making the inner space of ERp44 more accessible to Prx4.
Cross-references: PDB:5HQP
Protein: DP02173 (UniProt Q9BS26)
Region: residues 380	to 401
Annotation: order to disorder (Structural transition)
Evidence: combinatorial experimental and author inference evidence used in manual assertion
Supporting statements:
The intact ERp44 molecule (chain C, Figure 3) in the complex was taken for further structural comparison with free ERp44 (Figure 4), which clearly shows that the C-tail and even domain b′ in free ERp44 block the access of Prx4 by steric hindrance. When bound to Prx4, the three thioredoxin domains remain in the typical clover-like structure but with domain b′ rotated ∼40° anticlockwise relative to domain b. Moreover, the flexible C-tail (residues 351–372) becomes disordered with its electron density untraceable. The movements of the C-tail and the b′ domain disrupt the interactions among domains a, b′ and the C-tail, favoring an open conformation, thus making the inner space of ERp44 more accessible to Prx4.
 In the complex, the b′ domain in chain C rotates ∼40° and the visible part of the C-tail (residues 351–372) in free ERp44 colored in green becomes untraceable.
Cross-references: PDB:5HQP
Protein: DP02173 (UniProt Q9BS26)
Region: residues 380	to 401
Annotation: self-regulatory activity (Disorder function)
Evidence: combinatorial experimental and author inference evidence used in manual assertion
Supporting statements:
The intact ERp44 molecule (chain C, Figure 3) in the complex was taken for further structural comparison with free ERp44 (Figure 4), which clearly shows that the C-tail and even domain b′ in free ERp44 block the access of Prx4 by steric hindrance. When bound to Prx4, the three thioredoxin domains remain in the typical clover-like structure but with domain b′ rotated ∼40° anticlockwise relative to domain b. Moreover, the flexible C-tail (residues 351–372) becomes disordered with its electron density untraceable. The movements of the C-tail and the b′ domain disrupt the interactions among domains a, b′ and the C-tail, favoring an open conformation, thus making the inner space of ERp44 more accessible to Prx4.
The first structure we solved portrayed ERp44 in its inactive state and revealed that C-tail movements regulate substrate binding and release (Wang et al., 2008). 
Cross-references: PDB:5HQP
Protein: DP02188 (UniProt P52695)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three residues could not be located at the C-terminal end and varying regions (10–13 residues) are found to be disordered at the N-termini of different subunits indicating the flexibility of these ends.
Cross-references: PDB:4OOI
Protein: DP02188 (UniProt P52695)
Region: residues 1	to 10
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
While only 4 residues are missing in the α1 helix in HlyU_Vv, the N-terminus of HlyU_Vc appears to be more flexible (10–13 residues could not be traced).
Cross-references: PDB:4OOI
Protein: DP02191 (UniProt P51965)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the
crystal structure of UBE2E1, most of the N-terminal
residues are missing, suggesting that they were
flexible (Fig. 2a) and analysis of the sequence using
IUPred indicates that they have features expected
for disordered regions.
Protein: DP02191 (UniProt P51965)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In support of this, the N-terminal residues of UBE2E1 were sensitive to proteolytic cleavage.
Protein: DP02191 (UniProt P51965)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
and circular dichroism (CD) spectroscopy (Fig. 2e)
showed that the mean residue ellipticity for E2E1full
is decreased relative to E2E1core. Notably, the mean
residue ellipticity at 208 and 222 nM is reduced by
~ 20% in the E2E1full spectra, consistent with the
absence of regions of α-helical and β-sheet structure
in the 40 N-terminal residues.
Protein: DP02192 (UniProt O00571)
Region: residues 1	to 167
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The N-terminal region of DDX3 (1–167) was presumed to be unstructured, and a circular dichroism (CD) analysis supports this prediction.
Protein: DP02193 (UniProt P21734)
Region: residues 150	to 172
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The
three-dimensional structure of Ubc1 was determined by NMR
spectroscopy using standard triple resonance and 15N-edited, 13C-edited, and methyl-specific NOE experiments. A family of
21 structures was chosen (Fig. 1) based on their low energy and
the absence of distance violations (Table I). The structure of
Ubc1 contains two individually well defined domains tethered
by a 22-residue linker.
Protein: DP02193 (UniProt P21734)
Region: residues 150	to 172
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The three-dimensional structure of Ubc1 was determined by NMR spectroscopy using standard triple resonance and 15N-edited, 13C-edited, and methyl-specific NOE experiments. A family of 21 structures was chosen (Fig. 1) based on their low energy and the absence of distance violations (Table I). The structure of Ubc1 contains two individually well defined domains tethered by a 22-residue linker.
Cross-references: BMRB:6202
PDB:1TTE
Protein: DP02194 (UniProt P68466)
Region: residues 83	to 94
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered regions correspond to residues 83–94 and 116–128 (α5–α6 loop).
Elevated R1 rates and lower 15N{1H} NOE values measured in the loop 83–94 show that nanosecond time scale internal motions are also present, suggesting that K7 has substantial flexibility in this region relative to other viral and cellular Bcl-2 proteins.
Cross-references: PDB:2K36
BMRB:15740
Protein: DP02194 (UniProt P68466)
Region: residues 116	to 128
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered regions correspond to residues 83–94 and 116–128 (α5–α6 loop).
Cross peaks in the 1H–15N heteronuclear single quantum coherence (HSQC) for one of the regions in the protein (residues 116–128, α5–α6 loop) were relatively weak. In this region, peaks for residues F122, Q123, S124, L125 and I128 were missing from the spectra and could not be assigned, suggesting conformational exchange.
Cross-references: PDB:2K36
BMRB:15740
Protein: DP02194 (UniProt P68466)
Region: residues 118	to 127
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR structure of K7 revealed considerable flexibility in the region 118–127, which is an α helix (α6) in all other known viral and cellular Bcl-2 proteins.
Protein: DP02194 (UniProt P68466)
Region: residues 118	to 127
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The hydrophobic binding pocket in K7 is bordered by the N terminus (Tyr7), α1, and the region 118–127, which is predominantly nonhelical but is labeled “α6” to remain consistent with the canonical Bcl-2 fold. Despite lacking secondary structure, the backbone in this segment is well ordered in electron density maps.
Cross-references: PDB:3JRV
Protein: DP02195 (UniProt P53136)
Region: residues 434	to 463
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Nsa1 is suitable for a hybrid structural approach because it contains a well-structured WD40 domain followed by a functional, but flexible Cterminus
which is not amenable to X-ray crystallography methods. Following is a protocol for the cloning, expression, and purification of S.
cerevisiae Nsa1 for hybrid structural determination by X-ray crystallography and SAXS.
Protein: DP02196 (UniProt P37455)
Region: residues 107	to 171
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Since removal of the CTD moved the peak, this confirms that it is exclusively the CTDs (residues 107–171) that
contribute to this flexibility in solution. This result is in line with previous observations that the SSB CTD
has flexible properties
Protein: DP02196 (UniProt P37455)
Region: residues 107	to 171
Annotation: disorder (Structural state)
Evidence: small-angle neutron scattering evidence used in manual assertion
Supporting statements:
Since removal of the CTD moved the peak, this confirms that it is exclusively the CTDs (residues 107–171) that
contribute to this flexibility in solution. This result is in line with previous observations that the SSB CTD
has flexible properties