LiteFold/DisProt huggingface dataset:
Protein: DP02590 (UniProt P47523)
Region: residues 469	to 556
Annotation: flexible C-terminal tail (Disorder function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
The N- and C-terminal fragments (residues 37 to 74 and residues 469 to 556), which were truncated in Protein M TD as compared with Protein M, are likely disordered because the three-dimensional reconstructions of a Fab in complex with Protein M and Protein M TD by using negative-stain electron microscopy are nearly identical
These structural studies suggested that Protein M should preclude the ability of the antibody to bind to its antigen because it displaces or distorts the CDRs and/or may use its C-terminal domain to sterically block entrance to the antibody-combining site
Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens.
Protein: DP02591 (UniProt P78362)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
a comparison between ΔNΔS-SRPK2 (4.5 mg/mL black line) and SRPK2 (0.16 mg/mL blue line) samples indicates that the polydisperse full-length version in solution contains disordered regions, which are the ones that lack in the truncated version.
The scattering adjustment and pair-distribution function (Fig. 5) clearly depicts an elongated molecule profile in solution, because of the left side shift of the peak, as well as the tail on the q higher values [38]. The molecular dimensions RG (radius of gyration) and Dmax (maximum dimension) agree with each other between Guinier fit and p(r) calculations (Table 3). This elongated profile may suggest the contribution of the intrinsically unstructured regions SID and N-terminal for the oligomer formation.
Protein: DP02591 (UniProt P78362)
Region: residues 231	to 511
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
a comparison between ΔNΔS-SRPK2 (4.5 mg/mL black line) and SRPK2 (0.16 mg/mL blue line) samples indicates that the polydisperse full-length version in solution contains disordered regions, which are the ones that lack in the truncated version.
The scattering adjustment and pair-distribution function (Fig. 5) clearly depicts an elongated molecule profile in solution, because of the left side shift of the peak, as well as the tail on the q higher values [38]. The molecular dimensions RG (radius of gyration) and Dmax (maximum dimension) agree with each other between Guinier fit and p(r) calculations (Table 3). This elongated profile may suggest the contribution of the intrinsically unstructured regions SID and N-terminal for the oligomer formation.
Protein: DP02591 (UniProt P78362)
Region: residues 231	to 511
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD analysis (Fig. 4C, Table 2) also revealed that SRPK2 is composed of random structure with some content of regular secondary structure. These data agree with a model where the bi-lobed folded kinase domain somehow coexists with the intrinsically unstructured segments
Protein: DP02591 (UniProt P78362)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD analysis (Fig. 4C, Table 2) also revealed that SRPK2 is composed of random structure with some content of regular secondary structure. These data agree with a model where the bi-lobed folded kinase domain somehow coexists with the intrinsically unstructured segments
Protein: DP02591 (UniProt P78362)
Region: residues 231	to 511
Annotation: molecular function activator activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
the bi-lobed folded kinase domain somehow coexists with the intrinsically unstructured segments, which act as binding regions for other proteins [19] and contribute to the kinase processive activity over its substrates [18,41]. It is worth mentioning that the full-length kinase was quite active under in vitro experiments in our hands (data not shown).
In addition, together with an also intrinsically unstructured N-terminal extension, SID plays a critical role in the kinase processivity ability. This is mainly reached due to the N-terminal and SID nucleotide release factor action, which favors the ADP release from the active site during the catalysis [21].
Protein: DP02591 (UniProt P78362)
Region: residues 1	to 80
Annotation: molecular function activator activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
the bi-lobed folded kinase domain somehow coexists with the intrinsically unstructured segments, which act as binding regions for other proteins [19] and contribute to the kinase processive activity over its substrates [18,41]. It is worth mentioning that the full-length kinase was quite active under in vitro experiments in our hands (data not shown).
In addition, together with an also intrinsically unstructured N-terminal extension, SID plays a critical role in the kinase processivity ability. This is mainly reached due to the N-terminal and SID nucleotide release factor action, which favors the ADP release from the active site during the catalysis [21].
Protein: DP02591 (UniProt P78362)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In the aSEC experiments (Fig. 8A), the full-length SRPK2 was eluted with 11.5 mL, which is consistent with an apparent molecular mass equal to 220 ± 10 kDa. This value indicates species ranging between dimer and trimer species. The RS was determined to be 50 ± 1 Å, which yielded an f/f0 of 1.7 ± 0.1 (considering a monomeric form for SRPK2), indicating a highly elongated particle [46]. This shape could be due to the presence of unstructured regions in the full-length recombinant protein. The RG/RS ranging from 1.3 to 1.5 also suggests the presence of unstructured regions [37].
Protein: DP02591 (UniProt P78362)
Region: residues 231	to 511
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
In the aSEC experiments (Fig. 8A), the full-length SRPK2 was eluted with 11.5 mL, which is consistent with an apparent molecular mass equal to 220 ± 10 kDa. This value indicates species ranging between dimer and trimer species. The RS was determined to be 50 ± 1 Å, which yielded an f/f0 of 1.7 ± 0.1 (considering a monomeric form for SRPK2), indicating a highly elongated particle [46]. This shape could be due to the presence of unstructured regions in the full-length recombinant protein. The RG/RS ranging from 1.3 to 1.5 also suggests the presence of unstructured regions [37].
Protein: DP02591 (UniProt P78362)
Region: residues 231	to 511
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The f/f0 values were calculated to be 1.64 ± 0.03 for the monomer and 1.51 ± 0.04 for the dimer, which corroborates the hypothesis that SRPK2, either the monomer or the dimer, presents an elongated shape [32], likely due to the unstructured regions, as indicated by the aSEC experiments.
Protein: DP02591 (UniProt P78362)
Region: residues 1	to 80
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The f/f0 values were calculated to be 1.64 ± 0.03 for the monomer and 1.51 ± 0.04 for the dimer, which corroborates the hypothesis that SRPK2, either the monomer or the dimer, presents an elongated shape [32], likely due to the unstructured regions, as indicated by the aSEC experiments.
Protein: DP02592 (UniProt Q9H8Y8)
Region: residues 209	to 452
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum showed that the GRASP55 exhibited broad bands at ~203 and ~222 nm, suggesting the presence of the disordered as well as ordered secondary structure elements in the protein. The CD spectrum was further analyzed via CDSSTR routine using a set of various databases at Dichroweb server [33,34]. The results from CDSSTR deconvolution showed that fulllength GRASP55 has ~21% of α-helix, ~20% of β-sheet, ~17% of turns, and ~42% of disordered regions with the normalized root mean square deviation (NRMSD) of 0.19, which indicates, as already mentioned above, the presence of multiple disorder sites alongside well-structured regions. In addition, the protein family database analysis showed that the
full-length GRASP55 consists, as expected, of two domains: the GRASP (residues 1 –208) [17], including the two PDZ subdomains, and the SPR (residues 209 –452). Furthermore, the sequence-based prediction of protein disorder suggested that the C-terminal (SPR) domain of
full-length GRASP55 has high propensity of intrinsic disorder (Fig. 2), which is similar to the SPR domains of the CnGRASP and ScGRASP [29,30].
Based on these values, GRASP55 has Rh (measured from SEC-MALS) of the pre-molten globular conformation state. However, the far-UV CD studies and the crystal structure of the GRASP55 domain [17] showed that GRASP55 has a significant content of secondary structure in the native state. Moreover, the urea-induced denaturation studies showed that GRASP55
unfolds at high concentration (4 M) in a cooperative manner. These observations together suggest GRASP55 would not likely form a pre-molten globular conformation in the native conditions. It would rather either form a complex elongated conformation and/or its PDZ domains, influenced by the hydrophobic disordered Cterminal domain, would not fold properly.
Protein: DP02592 (UniProt Q9H8Y8)
Region: residues 209	to 452
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Furthermore, the obtained Rh value of GRASP55 is much higher than what is expected for
a ~47 kDa protein (~3 nm) [40,41 ] based on the relation between Rh and molecular mass of different standard proteins. This is another indication that GRASP55 exhibits intrinsically disorder (ID) behavior in solution and agrees with our findings mentioned above. The ID behavior previously observed for lower eukaryotic GRASPs [29,30] thus seems to be a general property of GRASPs, spanning from lower to higher eukaryotes.
Based on these values, GRASP55 has Rh (measured from SEC-MALS) of the pre-molten globular conformation state. However, the far-UV CD studies and the crystal structure of the GRASP55 domain [17] showed that GRASP55 has a significant content of secondary structure in the native state. Moreover, the urea-induced denaturation studies showed that GRASP55
unfolds at high concentration (4 M) in a cooperative manner. These observations together suggest GRASP55 would not likely form a pre-molten globular conformation in the native conditions. It would rather either form a complex elongated conformation and/or its PDZ domains, influenced by the hydrophobic disordered Cterminal domain, would not fold properly.
Protein: DP02592 (UniProt Q9H8Y8)
Region: residues 209	to 452
Annotation: phosphorylation display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Golgi structure formation is regulated by phosphorylation during the cell cycle. GRASP65 is a major target of mitotic kinases on the Golgi (Wang et al., 2003); the SPR domain contains multiple phosphorylation sites that are phosphorylated by Cdk1 and Plk in mitosis (Tang et al., 2012), which inhibits GRASP oligomerization and results in Golgi disassembly (Wang et al., 2005). At the end of mitosis, GRASP65 dephosphorylation by PP2A (Tang et al., 2008) allows the reformation of GRASP trans-oligomers and restacking of newly formed cisternae (Tang et al., 2010). GRASP55 is regulated in a similar way (Xiang and Wang, 2010), though phosphorylated by the MAP kinase ERKs instead (Jesch et al., 2001; Feinstein and Linstedt, 2007; Duran et al., 2008).
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 241	to 260
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis by trypsin or chymotrypsin did not compromise the integrity of the heterotrimeric complex (Fig. 1b). It also left eIF5A and Ran intact, but cleaved Xpo4 within two poorly conserved loops comprising residues 241–260 and 931–948, respectively
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 931	to 948
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis by trypsin or chymotrypsin did not compromise the integrity of the heterotrimeric complex (Fig. 1b). It also left eIF5A and Ran intact, but cleaved Xpo4 within two poorly conserved loops comprising residues 241–260 and 931–948, respectively
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 170	to 181
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 507	to 530
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 761	to 771
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 1034	to 1046
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 1034	to 1046
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
disordered region connecting repeats HEAT18B and HEAT19A
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 761	to 771
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
disordered region connecting repeats HEAT13B and HEAT14A
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 507	to 530
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
disordered region connecting repeats HEAT10A and HEAT10B
Cross-references: PDB:5DLQ
Protein: DP02593 (UniProt Q9ESJ0)
Region: residues 170	to 181
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes residues 7–179 of Ran and 15–152 of eIF5A. We modelled 1,052 of 1,113 residues of Xpo4, with a few residues missing from N- and C-terminus as well as from several loop regions between the HEAT repeats.
disordered region connecting repeats HEAT4B and HEAT5A
Cross-references: PDB:5DLQ
Protein: DP02594 (UniProt P63241)
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:
Even though this complex was stable and monodisperse, it did not crystallize–apparently because of disordered loops and termini: Indeed, the 14 N-terminal probably disordered residues of eIF5A (refs 36, 37, 53) not only turned out to be dispensable for complex formation (Fig. 1a), but also, their deletion allowed the RanGTP·Xpo4·eIF5A complex to crystallize in needle clusters.
Cross-references: PDB:5DLQ
Protein: DP02595 (UniProt P25490)
Region: residues 1	to 295
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The discrepancy between the formula and SDS-PAGE-determined molecular masses suggests that YY1 belongs to the group of Intrinsically Disordered Proteins (IDPs). In general, the apparent molecular masses of IDPs determined by SDSPAGE are 1.2 – 1.8 times higher than the results expected from sequence data or measured by mass spectrometry.45 The retarded IDP mobility by SDS-PAGE results from IDPs binding less SDS than globular proteins because of their decreased hydrophobic residue content.
Analogous calculations conducted for the DBD showed migration typical for a globular protein (the formula and apparent molecular masses calculated from electrophoresis are 14,053.9 Da and 14 kDa, respectively). Furthermore, considering that the apparent molecular masses of full-length YY1 and its N-terminal fragment were 1.23 and 1.38 times higher, respectively, than their formula masses, the studied proteins appear to have strongly heterogeneous and complex structures, and the intrinsically disordered properties are primarily in the N-terminal fragment of the protein. This observation justifies the division of the YY1 protein into N- and C-terminal fragments around the 295 residue and also justifies studying them separately.
Protein: DP02595 (UniProt P25490)
Region: residues 1	to 295
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
YY1, the NTF and casein were efficiently digested by both enzymes under moderate conditions (30 min at 25 8C at 1:500 protease/substrate ratio), whereas the DBD and
BSA were not. The NTF exhibited the greatest susceptibility to proteolysis, and the process was almost complete with the use of proteinase K.
Protein: DP02595 (UniProt P25490)
Region: residues 1	to 295
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
According to the presented data, the DBD can be classified as a globular protein or molten globule (Rs 5 20.5 A˚ 34), and the NTF (Rs 5 46.8 A˚ ) can be classified as a random coil under native conditions. Surprisingly, the hydrodynamic radius of full-length YY1
(Rs 5 46.5 A˚ ) is slightly lower than that of its N-terminal part and may indicate a pre-molten globule or random coil state under native conditions.
Protein: DP02595 (UniProt P25490)
Region: residues 1	to 295
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectrum registered for the DBD is typical for C2H2-type zinc finger structures ligated with Zn21,62,63 and the spectra obtained for YY1 and its N-terminal
fragment are typical for proteins with a low content of stable secondary structures, that is, for IDPs.38,64
Protein: DP02595 (UniProt P25490)
Region: residues 1	to 295
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Similar conclusions can be drawn from the analysis of the fluorescence spectra recorded for two tryptophan residues present in the protein (W205 and W225). Under native conditions, the maximum fluorescence emission wavelength was approximately 340 nm (Fig. 7), compared with the range of 346–350 nm for water-exposed tryptophan residues in proteins (Class III, according to tryptophan residue classification).67
Protein: DP02596 (UniProt Q04866)
Region: residues 206	to 249
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loop connecting helices α6 and α7, the loop between helices α4 and α5, and the loop that connects the β2-β3 strands each have disordered segments in one or more of the structures.
Region 206-249 of WzzB from Salmonella typhimurium connects helices α6 and α8 of the protein and corresponds to a disordered region not visible in the electron density (see Supplementary Figure S1)
Cross-references: PDB:3B8P
Protein: DP02597 (UniProt O49195)
Region: residues 16	to 48
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the final model, the electron density of residues Val16-Glu48 was invisible, and therefore, these residues were excluded.
Cross-references: PDB:4FYP
Protein: DP02598 (UniProt Q96H20)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 149–169 from VPS36 and residues 1–25 from VPS22 are present in construct a, but could not be visualized in electron density and are presumed to be disordered.
Authors of the publication refer to the N-terminal 25 residues of VPS22 as VPS22-H0
Cross-references: PDB:2ZME
PDB:3CUQ
Protein: DP02598 (UniProt Q96H20)
Region: residues 1	to 25
Annotation: lipid binding (Molecular function)
Evidence: co-sedimentation assay evidence used in manual assertion
Supporting statements:
Authors of the publication refer to the N-terminal 25 residues of VPS22 as VPS22-H0
The observation that both the Vps36 GLUE domain and the Vps22 H0 contribute to lipid binding in vitro suggested to us that a combinatorial mechanism evolved to drive high-affinity membrane targeting of ESCRT-II
The purified pseudo-intact ESCRT-II showed strong binding to liposomes made of synthetic lipids composed of phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphoinositides (PIPs) (Fig. 4D–K), and bound weakly to PC:PE and PC:PE:phosphatidylinositol (PI) liposomes (Fig. 4B, C, K).