LiteFold/DisProt huggingface dataset:
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 980	to 1009
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We modeled 1082 of 1204 residues of Exp-5. Several loop regions in the 20 HEAT repeats and 55 residues at the C terminus could not be modeled (details in fig. S1), and 13 residues at the C terminus were modeled as a polyalanine a helix.
he N-terminal residue 1, residues 474-490 in the loop of HEAT12, residues 705-706 in the loop of HEAT14, residues 938-951 in the loop of HEAT17 and residues 980-1069 in the loop between HEAT17 and HEAT18 are disordered in the crystal. Out of 68 C-terminal residues, 55 residues were not modeled because of disordered structure, and 13 residues were built as a poly-alanine α-helix because of high temperature factor.
This feature corresponds to the IDR in the loop between HEAT17 and HEAT18  as shown in Supplementary Fig. S1. The respective author statement, taken from the legend of Fig. S1, erroneously refers to the range of this IDR as 980-1069. See Supplementary Fig. S1 and the respective PDB entry (PDB:3A6P) for more details.

Cross-references: PDB:3A6P
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 1137	to 1191
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We modeled 1082 of 1204 residues of Exp-5. Several loop regions in the 20 HEAT repeats and 55 residues at the C terminus could not be modeled (details in fig. S1), and 13 residues at the C terminus were modeled as a polyalanine a helix.
The N-terminal residue 1, residues 474-490 in the loop of HEAT12, residues 705-706 in the loop of HEAT14, residues 938-951 in the loop of HEAT17 and residues 980-1069 in the loop between HEAT17 and HEAT18 are disordered in the crystal. Out of 68 C-terminal residues, 55 residues were not modeled because of disordered structure, and 13 residues were built as a poly-alanine α-helix because of high temperature factor.
This feature corresponds to the 55 disordered residues within the 68 residue long C-terminal segment mentioned in Supplementary Fig. S1.
Cross-references: PDB:3A6P
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 1180	to 1204
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 25 C-terminal residues (residues 1,180–1,204) could not be traced in all three Exp-5 structures (Figure 1E).
Figure 1E. The secondary structure of the C-terminal area of Exp-5 alone and Exp-5 complexes. C-terminal 1,180–1,204 residues (light gray) are not shown in all Exp-5 structures.
Cross-references: PDB:5YU7
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 1180	to 1204
Annotation: RNA binding (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
On the other hand, the last 25 ‘‘C-terminal end’’ (residues 1,180–1,204) might not be keenly involved in the stabilization of the protein based on X-ray structures because C-terminal end residues showed no electron density for Exp-5 structures at three states: Exp-5 alone, the binary complex, and the ternary complex. Interestingly, the C-terminal end has shown important biological functions involved in the binding and/or recognition of pre-miRNAs as cargo substrate (Melo et al., 2010).
Cross-references: PDB:5YU6
PDB:5YU7
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 478	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Not explicitly mentioned in the manuscript, but reported within the PDB file (under REMARK 465 MISSING RESIDUES).
Cross-references: PDB:5YU7
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 474	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Not explicitly mentioned in the manuscript, but reported within the PDB file (under REMARK 465 MISSING RESIDUES).
Cross-references: PDB:5YU6
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 1167	to 1179
Annotation: order to disorder (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The interaction site of the C-terminal anchor with HEATs 4–9 in Exp-5 alone overlaps with the RanGTP binding site at the N-terminal HEATs of Exp-5 of the binary complex. The interaction between the C-terminal anchor and the N-terminal HEATs of Exp-5 is likely to be important in stabilizing the closed conformation of Exp-5 alone.
The 'C-terminal anchor' segment is ordered in the monomeric form of Exp-5 (5YU7), while it is disordered in the oligomeric forms Exp-5:RanGTP (5YU7), Exp-5:RanGTP:pre-miRNA (PDB:3A6P, PMID:19965479).

To accommodate RanGTP, intramolecular interaction between the C-terminal anchor and HEATs 4–9 of Exp-5 should be removed (Figure 3). For this motion, a notable key region is in the last 24 amino acids at the C-terminal end of Exp-5.
Cross-references: PDB:5YU7
PDB:5YU6
Protein: DP03195 (UniProt Q9HAV4)
Region: residues 938	to 951
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Not explicitly mentioned in the manuscript, but reported within the PDB file (under REMARK 465 MISSING RESIDUES).
Cross-references: PDB:5YU6
Protein: DP03196 (UniProt Q8N1Q8)
Region: residues 102	to 111
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Them4 and Them5 proteins contain a highly variable sequence stretch (ca. residues 83 to 109 and ca. residues 91 to 114 for Them4 and Them5, respectively) that is partially disordered in both crystal structures.
PDB structure (https://files.rcsb.org/pub/pdb/validation_reports/ae/4ae7/4ae7_full_validation.pdf) shows that region 102-111 is disordered.
Cross-references: PDB:4AE7
Protein: DP03197 (UniProt P41209)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Twenty-five amino acids from the N-terminus in the crystal structure, which was interpretable and used to build a structural model of residues L26 to Y172, were not modeled because of high flexibility. 
Cross-references: PDB:5D43
Protein: DP03198 (UniProt P62696)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, it was not possible to model the first 13 residues of the N-terminal extension of βB2-N, nor linker residues 85 to 88, in either molecule of βB2-N, suggesting a disordered conformation for the N-terminal extension and residues 85 to 88.
Cross-references: PDB:1E7N
Protein: DP03199 (UniProt P00749)
Region: residues 21	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to a disorder, residues 1–10 and 133–143 are not modeled in the final structure.
Additionally, due to a lack of the interpretable electron density peaks, residues 1–10 and 133–143 of ATF and 108–111, 134–138, and 248–251 of suPAR 2345 are not included in the final model.
The disordered region described in the publication comprises residues 1-10 which maps to region 21-30 of the UniProt amino acid sequence, since the latter includes a natural signal peptide (1-20) that is cleaved in the mature protein.
Cross-references: PDB:2I9A
PDB:2I9B
Protein: DP03199 (UniProt P00749)
Region: residues 153	to 163
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to a disorder, residues 1–10 and 133–143 are not modeled in the final structure.
Additionally, due to a lack of the interpretable electron density peaks, residues 1–10 and 133–143 of ATF and 108–111, 134–138, and 248–251 of suPAR 2345 are not included in the final model.
The disordered region described in the publication comprises residues 133-143 which maps to region 153-163 of the UniProt amino acid sequence, since the latter includes a natural signal peptide (1-20) that is cleaved in the mature protein.
Cross-references: PDB:2I9A
PDB:2I9B
Protein: DP03200 (UniProt P04711)
Region: residues 124	to 140
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal region (residues 1–34) and three loops comprising residues 124–140, 761–768, and 928–935 in the structure of ZmPEPC show little or no electron density (Figure 1E). Since there was no significant cleavage, as judged by SDS-PAGE [17], it is apparent that the three loops exist in multiple conformations, whereas only the N-terminal region is partially truncated.
Cross-references: PDB:1JQO
Protein: DP03201 (UniProt Q96CV9)
Region: residues 416	to 442
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we used the OPTN CC2-UBAN region for crystallization experiments, the electron density for the majority of the CC2 region in all OPTN molecules was very weak and thus we modelled only the UBAN motif with some extensions on both sides (residues 445–505 for the longest chain).
Cross-references: PDB:5B83
Protein: DP03203 (UniProt P55210)
Region: residues 197	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final refined model contains residues 58–196, 211–303 for chain A and 57–196, 211–304 for chain B.
Cross-references: PDB:3H1P
Protein: DP03203 (UniProt P55210)
Region: residues 197	to 211
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined model of Csp7 contains a complete catalytic unit comprising two p20–p10 heterodimers. The p20 and p10 polypeptide chains are composed of residues 57–196 and 212–302, respectively. 
Cross-references: PDB:1F1J
Protein: DP03203 (UniProt P55210)
Region: residues 197	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final atomic model contains residues 55–196 and 211–303 from the first caspase-7 protomer, residues 58–196 and 211–303 from the second caspase-7 protomer, and residues 134–150 for both bound XIAP linkers.
Cross-references: PDB:1I4O
Protein: DP03204 (UniProt Q16629)
Region: residues 81	to 98
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The narrow signal linewidth and small
chemical shift dispersion observed in the 1
H-15N-correlated
(HSQC) NMR spectrum reveal that the C-terminal argininerich region, required for TAP binding (Figure 1A and below),
is unstructured and highly flexible.
Cross-references: PDB:2HVZ
Protein: DP03204 (UniProt Q16629)
Region: residues 81	to 98
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
A similar analysis was undertaken with 9G8 and it was
shown that a short arginine-rich peptide (aa 81–98), which
lies between the RRM and the zinc-knuckle, was sufficient
for interaction with TAP-p15 (Figure 4D–F). Within this
sequence, the arginine dipeptides at positions 87, 88 and
97, 98 were required for the interaction, whereas Arg 90, 93
were not. These data indicate that 9G8 and SRp20 harbor
a TAP-binding motif, which consists of an arginine-rich
peptide, which from the NMR analysis, appears flexible and
is tightly juxtaposed with their RRMs.
Protein: DP03204 (UniProt Q16629)
Region: residues 123	to 176
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This poly-E region is inferred by the curator to be disordered, based on MobiDB-Lite and according to experimental evidence demonstrating that poly-E repeats display random-coil-like conformation (PMID:16949547)
Protein: DP03204 (UniProt Q16629)
Region: residues 200	to 217
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This poly-E region is inferred by the curator to be disordered, based on MobiDB-Lite and according to experimental evidence demonstrating that poly-E repeats display random-coil-like conformation (PMID:16949547)
Protein: DP03205 (UniProt O95696)
Region: residues 63	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, only the central portion of the
BRPF2 fragment (residues 39–62) is visible; both the Nterminal and C-terminal regions are disordered.
Cross-references: PDB:5GK9
Protein: DP03206 (UniProt Q8IYB8)
Region: residues 47	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct of hSuv3 used for crystallization contained
residues 47–722 of the complete genome sequence plus an
additional Gly at the N-terminus. In both crystal structures
fragments of the N- and C-termini (residues 46–57 and 690–
722), as well as two other fragments of the chain (73–86 and
446–456), are disordered and are not visible in the electrondensity map.
Cross-references: PDB:3RC8
PDB:3RC3
Protein: DP03206 (UniProt Q8IYB8)
Region: residues 73	to 86
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct of hSuv3 used for crystallization contained
residues 47–722 of the complete genome sequence plus an
additional Gly at the N-terminus. In both crystal structures
fragments of the N- and C-termini (residues 46–57 and 690–
722), as well as two other fragments of the chain (73–86 and
446–456), are disordered and are not visible in the electrondensity map.
Cross-references: PDB:3RC8
PDB:3RC3
Protein: DP03206 (UniProt Q8IYB8)
Region: residues 446	to 456
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct of hSuv3 used for crystallization contained
residues 47–722 of the complete genome sequence plus an
additional Gly at the N-terminus. In both crystal structures
fragments of the N- and C-termini (residues 46–57 and 690–
722), as well as two other fragments of the chain (73–86 and
446–456), are disordered and are not visible in the electrondensity map.
Cross-references: PDB:3RC8
PDB:3RC3
Protein: DP03206 (UniProt Q8IYB8)
Region: residues 690	to 722
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct of hSuv3 used for crystallization contained
residues 47–722 of the complete genome sequence plus an
additional Gly at the N-terminus. In both crystal structures
fragments of the N- and C-termini (residues 46–57 and 690–
722), as well as two other fragments of the chain (73–86 and
446–456), are disordered and are not visible in the electrondensity map.
Cross-references: PDB:3RC8
PDB:3RC3
Protein: DP03207 (UniProt Q8IYV9)
Region: residues 257	to 268
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 Residues 257-268 in Izumo122-268 are disordered suggesting that the linker region between the Ig-like domain and the transmembrane domain is highly flexible.
The Izumo122-268 structure superimposes well with Izumo122-254 (rmsd 1.0-Å over all atoms) (Supplementary Fig. 4). However, no electron density was observed after residue 256, suggesting that the linker region following the Ig-like domain is flexible.
Cross-references: PDB:5F4T
Protein: DP03207 (UniProt Q8IYV9)
Region: residues 127	to 140
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
Moreover, DXMS experiments performed
on Izumo1 alone indicated a high level of exchange in the hinge region, thus suggesting
dynamic flexible motion within this region. Upon Juno binding, deuterium exchange of
residues 127-140 in the hinge region was reduced by >50%, which is more than the
reduction seen by residues at the Izumo1-Juno interface (Fig. 4). The strong level of H/D
protection is due to the formation of 10 additional main chain hydrogen bonds within
residues 127-140 of the hinge region. This suggests that the Izumo1 hinge region is
stabilized in a “locked” upright position in the presence of Juno
Protein: DP03209 (UniProt A6ND01)
Region: residues 111	to 122
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A disordered loop between the β1 and β2 strands of the Juno20-228 is shown with a black dashed line. 
The region corresponding to residues 111-122 corresponds to a missing residues region in the 5F4Q PDB structure
Cross-references: PDB:5F4Q
Protein: DP03209 (UniProt A6ND01)
Region: residues 111	to 122
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The human JUNO L2 region, which corresponds to the inhibitory loop in FRs11, is disordered (Fig. 2b), possibly due to a 6–7 amino acid insertion not present in other species (Extended Data Figs 1 and 2)
Cross-references: PDB:5JKA
Protein: DP03211 (UniProt Q9BRT9)
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:
No clear indication in the paper, atomic coordinates are missing from PDB file
Cross-references: PDB:2Q9Q
Protein: DP03212 (UniProt P0DTC9)
Region: residues 182	to 197
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Chemical shift analysis
showed that residues A182-S197 are very dynamic with a small propensity of α-helical structure next to R189
Fig 3b. clearly indicates that the region is intrinsically disordered
Protein: DP03212 (UniProt P0DTC9)
Region: residues 182	to 197
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR titrations showed that the unmodified SR-peptide strongly interacts with polyU
Protein: DP03212 (UniProt P0DTC9)
Region: residues 186	to 190
Annotation: molecular recognition display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SRPK1-phosphorylation resulted in two species, a single phosphorylation at S188 (Fig. 4b, middle) and a di-phosphorylated state, which is heterogeneously phosphorylated at four different serines (Fig. 4b, bottom; Supplementary Fig. 7). NMR titrations showed that the unmodified SR-peptide strongly interacts with polyU, but not when it is phosphorylated at S188 (Fig. 4b and Supplementary Fig. 4b). LLPS experiments further demonstrated that phosphorylation of full-length NSARS-CoV-2 by SRPK1 changes its RNA-induced phase separation behavior (Fig. 4c and Supplementary Fig. 8). The maximum of RNA- induced turbidity was shifted to lower polyU-concentrations for SRPK1-phosphorylated NSARS-CoV-2 (Fig. 4c). In addition, fluorescently labeled RNA was less recruited to droplets formed by SRPK1-phosphorylated NSARS-CoV-2 (Fig. 4d). In agreement with an attenuated interaction of NSARS-CoV-2 with RNA upon SRPK1-phosphorylation, we also observed a more rapid diffusion of SRPK1-phosphorylated NSARS-CoV-2 inside of polyU-induced droplets when compared to the unmodified protein (Fig. 4e). On the other hand, SRPK1-phosphorylated NSARS-CoV-2 still co-localized with stress granules (Fig. 4d).
The evidence refers to phosphorylated serine pS188.
Protein: DP03212 (UniProt P0DTC9)
Region: residues 182	to 197
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: turbidity measurement evidence used in manual assertion
Supporting statements:
SRPK1-phosphorylation resulted in two species, a single phosphorylation at S188 (Fig. 4b, middle) and a di-phosphorylated state, which is heterogeneously phosphorylated at four different serines (Fig. 4b, bottom; Supplementary Fig. 7). NMR titrations showed that the unmodified SR-peptide strongly interacts with polyU, but not when it is phosphorylated at S188 (Fig. 4b and Supplementary Fig. 4b). LLPS experiments further demonstrated that phosphorylation of full-length NSARS-CoV-2 by SRPK1 changes its RNA-induced phase separation behavior (Fig. 4c and Supplementary Fig. 8). The maximum of RNA-induced turbidity was shifted to lower polyU-concentrations for SRPK1-phosphorylated NSARS-CoV-2 (Fig. 4c). In addition, fluorescently labeled RNA was less recruited to droplets formed by SRPK1-phosphorylated NSARS-CoV-2 (Fig. 4d). In agreement with an attenuated interaction of NSARS-CoV-2 with RNA upon SRPK1-phosphorylation, we also observed a more rapid diffusion of SRPK1-phosphorylated NSARS-CoV-2 inside of polyU-induced droplets when compared to the unmodified protein (Fig. 4e).
Protein: DP03212 (UniProt P0DTC9)
Region: residues 182	to 197
Annotation: intracellular non-membrane-bounded organelle (Cellular component)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
SRPK1-phosphorylated NSARS-CoV-2 still co-localized with stress granules.
Association of unmodified (NSARS-CoV-2, left panels) and phosphorylated (phosphoNSARS-CoV-2, right panels) nucleocapsid protein of SARS-CoV-2 with stress granules in HeLa cells