LiteFold/DisProt huggingface dataset:
Protein: DP02122 (UniProt Q02199)
Region: residues 1	to 260
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Figure 3 and supplementary Movie S1 online show that hNup153FG hydrogels are formed from interlaced fibres that build up a meshwork giving rise to the supramolecular architecture of a hydrogel (see supplementary Fig S3 online; supplementary Movie S2 online for yNup49FG).
To exclude artifacts that might arise from sample preparation, we confirmed these results using alternative preparation and imaging methods, namely scanning electron microscopy of heavy metal-shaded samples (Fig 3; supplementary Fig S3 online), as well as transmission electron microscopy of frozen-hydrated cryosections (supplementary Fig S5 online). We consistently observed fibrous networks within the hydrogels.
Protein: DP02123 (UniProt P52948)
Region: residues 2	to 150
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Region is shown to be intrinsically disordered by smFRET and SAXS measurements
Cross-references: SASBDB:SASDEB3
Protein: DP02123 (UniProt P52948)
Region: residues 2	to 150
Annotation: disorder (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
Region is shown to be intrinsically disordered by smFRET and SAXS measurements
Protein: DP02123 (UniProt P52948)
Region: residues 1	to 730
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structures of the Human nuclear pore complex (both dilated and constricted), shows this region from the NUP98 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:7R5J
PDB:7R5K
EMDB:14322
EMDB:14321
Protein: DP02123 (UniProt P52948)
Region: residues 881	to 1111
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structures of the Human nuclear pore complex (both dilated and constricted), shows this region from the NUP98 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:7R5J
PDB:7R5K
EMDB:14322
EMDB:14321
Protein: DP02123 (UniProt P52948)
Region: residues 1161	to 1193
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structures of the Human nuclear pore complex (both dilated and constricted), shows this region from the NUP98 protein lacks electron density, indicating it is disordered.
Cross-references: PDB:7R5J
PDB:7R5K
EMDB:14322
EMDB:14321
Protein: DP02123 (UniProt P52948)
Region: residues 1	to 499
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
We next extended our analysis of spontaneous FG phase formation to the entire set of Nup98 FG domains. We observed that all of them showed the same readiness to phase-separate and form FG particles as the ScNup100 FG domain (Figures 6 and 7).
Protein: DP02123 (UniProt P52948)
Region: residues 1	to 499
Annotation: amyloid fibril formation (Biological process)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
Particles were formed at 5 µM (HsNup98, TtMacNup98, TbNup158) or 10 µM FG domain concentration (all other FG domains). The suspensions were afterwards supplemented with 3 µM MBP-mCherry and 1 µM ThioflavinT, a diagnostic dye for the presence of amyloid-like cross-β-structures.
Protein: DP02123 (UniProt P52948)
Region: residues 1	to 499
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
As a first step, we constructed bacterial expression vectors, and recombinantly expressed, purified, and immobilized all ten Nup98 domains. We observed that all of them bound human Importin β specifically and to a similar extend (Figure 5B).
Protein: DP02124 (UniProt Q03281)
Region: residues 99	to 140
Annotation: disorder (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
The region was demonstrated to be intrinsically disordered by smFRET as well as SAXS measurements
Protein: DP02124 (UniProt Q03281)
Region: residues 99	to 140
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The region was demonstrated to be intrinsically disordered by smFRET as well as SAXS measurements
Cross-references: SASBDB:SASDEM2
Protein: DP02126 (UniProt P30307)
Region: residues 208	to 225
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Protein crystallography, biophysical affinity determination and biomolecular simulations unanimously deliver a remarkable finding: a supramolecular "Janus" ligand can bind simultaneously to a flexible peptidic PPI recognition motif and to a well-structured adapter protein.
Cross-references: PDB:5M37
Protein: DP02126 (UniProt P30307)
Region: residues 208	to 225
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Upon binding to the rigid 14-3-3 protein, the recognition motifs undergo a disorder-to-order transition which might impose a specific functional fold of the IDP.
Protein: DP02126 (UniProt P30307)
Region: residues 208	to 225
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of the ternary complex between 14-3-3ζ, the Cdc25CpS216 peptide and CLR01 revealed that the molecular tweezer is bound to R208 of the Cdc25C peptide (R208Cdc25C).
Cross-references: uniprot:P31946
Protein: DP02127 (UniProt P0AG30)
Region: residues 1	to 30
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was evident for residues 31–354 of both Rho protomers and for three RNA segments. The final model has been refined to 3.5 A ̊ resolution and shows good stereochemistry.
This movement is concomitant with a loss of interpretable electron density for the first 30 amino acids at the extreme N terminus, a highly variable and typically Arg/Gly-rich region of Rho orthologs.
Cross-references: PDB:2HT1
Protein: DP02127 (UniProt P0AG30)
Region: residues 355	to 411
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was evident for residues 31–354 of both Rho protomers and for three RNA segments. The final model has been refined to 3.5 A ̊ resolution and shows good stereochemistry.
This movement is concomitant with a loss of interpretable electron density for the first 30 amino acids at the extreme N terminus, a highly variable and typically Arg/Gly-rich region of Rho orthologs. Another difference is that the last 65 amino acids of the C-terminal domain are disordered and have been displaced in part by residues from the connector loop that links the N- and C-terminal domains.
Since Phe355 lies within the C-terminal region of Rho that is disordered in this crystal form, and since Rho411 retains length-dependent RNA-stimulated ATPase activity.
Cross-references: PDB:2HT1
Protein: DP02128 (UniProt P06437)
Region: residues 31	to 102
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Trypsin cleavage before crystallization separates residues Ala31 to Arg102, which are poorly conserved and relatively unstructured, from the rest of the molecule, probably because this segment, which contains a heparan sulfate interaction site (23), is not firmly anchored.
Protein: DP02128 (UniProt P06437)
Region: residues 462	to 490
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Trypsin cleavage before crystallization separates residues Ala31 to Arg102, which are poorly conserved and relatively unstructured, from the rest of the molecule, probably because this segment, which contains a heparan sulfate interaction site (23), is not firmly anchored.
Cross-references: PDB:2GUM
Protein: DP02129 (UniProt O94444)
Region: residues 229	to 243
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, the crystallographic and NMR data suggest a structure for Rpn10 in which a compact VWA fold (residues 1–191) is connected via a long (approximately 16 amino acids), flexible linker to an extended α-helix that in solution does not interact with the VWA domain (Fig. 4C).
Protein: DP02129 (UniProt O94444)
Region: residues 192	to 209
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, the crystallographic and NMR data suggest a structure for Rpn10 in which a compact VWA fold (residues 1–191) is connected via a long (approximately 16 amino acids), flexible linker to an extended α-helix that in solution does not interact with the VWA domain (Fig. 4C).
Protein: DP02130 (UniProt P02671)
Region: residues 232	to 581
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In human fibrinogen α chains, there are ten 13-residue repeats that are absent in chicken fibrinogen. The repeat region and the αC domain are mostly disordered and cannot be discerned in electron density maps.
The flexibly attached and mobile αC domains, which cannot be identified in electron density maps, are only ∼30% identical in the two species.
As was the case for native chicken fibrinogen, no resolvable electron density could be associated with αC domains.
There was no discernible electron density corresponding to the αC domains.
Beyond that, the lack of electron density for regions corresponding to the αC domains, often termed “free swimming appendages”, is further testimony to the mobile nature of these entities (46), elegant NMR studies showing some core structure notwithstanding (47, 48).
As such, it is not surprising that in this study no density was found that could be assigned to αC domains with any certainty.
Cross-references: PDB:3GHG
Protein: DP02132 (UniProt P04386)
Region: residues 107	to 144
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the GCN4 fragment in buffered aqueous solution (pH 7.0) consists of a single negative absorption at 197nm, characteristic of a conformationally mobile species
Protein: DP02134 (UniProt P0ABS5)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Increased R1 and decreased R2 relaxation rates indicated increased mobility and structural disorder for about 12 and three residues at the N-terminus and C-terminus of the construct, respectively.
Cross-references: PDB:2haj
Protein: DP02137 (UniProt P0AGE0)
Region: residues 114	to 178
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA
The crystal structure of full-length homotetrameric single-stranded DNA (ssDNA)-binding protein from Escherichia coli (SSB) has been determined to 3.3 Å resolution and reveals that the entire C-terminal domain is disordered even in the presence of ssDNA.
Although the effective resolution of our analysis is a limiting 3.3 Å, the sharp contrast in electron density quality between the disordered C-terminal domain and the well-ordered core domain strongly suggests that our interpretation is qualitatively correct. Furthermore, the low-resolution diffraction of SSB-dC(pC)34 crystals is consistent with the observed molecular disorder and with the consensus that macromolecules with high degrees of flexibility and/or lack of regular structure either fail to crystallize or yield weakly diffracting crystals.
The core domain of SSB could be readily modeled in the experimental electron density maps up to residue 112 in each molecule, whereas the electron density of the anticipated C-terminal domain was undecipherable suggesting extreme disorder.
Cross-references: PDB:1SRU
Protein: DP02138 (UniProt P63159)
Region: residues 185	to 214
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The dynamic nature of the acidic IDR interaction with CXCL12 was further confirmed by NMR titrations of recombinant 15N acidic IDR (Acpeprec) with unlabelled CXCL12. As is typical for fuzzy interactions involving IDRs or intrinsically disordered proteins (IDPs) the 1H-15N HSQC spectrum of 15N Ac-peprec, in both the absence and presence of equimolar CXCL12, displayed reduced peak dispersion and high signal overlap, with minimal chemical shift perturbations (Fig. 4a).
Protein: DP02138 (UniProt P63159)
Region: residues 185	to 214
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We therefore focused our SAXS analysis on the sample comprising two CXCL12
equivalents. We observed an overall increase of the derived parameters with respect to free frHMGB1, compatible with complex formation (Rg of 2.93 nm and Dmax of 10.5 nm) and a mass estimation corresponding to frHMGB1•CXCL12 heterocomplex (Supplementary Fig. 8a). The normalized Kratky plot and the P(r) plot confirmed the dynamic and flexible nature of the complex, containing both folded domains and unstructured segments (Fig. 7b, Supplementary Fig. 8b).
Protein: DP02138 (UniProt P63159)
Region: residues 185	to 214
Annotation: protein heterodimerization activity (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We therefore focused our SAXS analysis on the sample comprising two CXCL12
equivalents. We observed an overall increase of the derived parameters with respect to free frHMGB1, compatible with complex formation (Rg of 2.93 nm and Dmax of 10.5 nm) and a mass estimation corresponding to frHMGB1•CXCL12 heterocomplex (Supplementary Fig. 8a). The normalized Kratky plot and the P(r) plot confirmed the dynamic and flexible nature of the complex, containing both folded domains and unstructured segments (Fig. 7b, Supplementary Fig. 8b).
Protein: DP02138 (UniProt P63159)
Region: residues 185	to 214
Annotation: protein heterodimerization activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, comparison of 15N CXCL12 NMR titrations with frHMGB1 fragments revealed that the acidic IDR of HMGB1 is directly involved in frHMGB1•CXCL12 heterocomplex formation and that the CXCL12 dimerization surface works as hub for multivalent interactions with both the acidic IDR and the HMG tandem domain.
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1244	to 1273
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-​-3,3, Table 3-​-5),5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues.
However, the marginal secondary structure content suggests that all the peptides tested are IDRs.
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1	to 172
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
Cross-references: PDB:8KBY
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 304	to 424
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
Cross-references: PDB:8KBY
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1237	to 1416
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
Cross-references: PDB:8KBY
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1736	to 1938
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
Cross-references: PDB:8KBY
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 204	to 220
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 464	to 483
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 617	to 628
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 747	to 793
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 850	to 923
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 940	to 957
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 996	to 1015
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1025	to 1041
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087