LiteFold/DisProt huggingface dataset:
Protein: DP02105 (UniProt P74518)
Region: residues 102	to 191
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The intrinsically disordered nature of C-LrtA was suggested by several pieces of evidence: (i) the lack of dispersion in NMR spectra (Figure 1); (ii) the shape (Figure 2A) and the deconvolution of far-UV CD spectrum; (iii) the absence of all-or-none co-operative transitions in the thermal and chemical denaturations (Figure 2B,C); and (iv) a model of the structure without the His-tag obtained with MD simulation (Figure 3).
Therefore, we can conclude from the far-UV CD data that C-LrtA was disordered.
Protein: DP02105 (UniProt P74518)
Region: residues 102	to 191
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Fluorescence spectra of C-LrtA showed a maximum at 307 nm, corresponding to its 4 tyrosine residues [20,21]. We carried out GdmCl denaturations by following the <λ> (at two different C-LrtA concentrations) after excitation at 280 nm. At both protein concentrations, we observed a linear decrease in the <λ> as the concentration of chemical denaturant was increased (Figure 2B, right axis, red circles). We could not fit these data to the linear extrapolation model, as fitting led to thermodynamic parameters (m- or [GdmCl]1/2-values) with non-physical meaning (i.e., either negative values or values higher than the protein concentration explored). A similar linear tendency was observed in thermal denaturations (Figure 2C, right axis, red circles). Therefore, we can conclude from the fluorescence data that C-LrtA was disordered.
The intrinsically disordered nature of C-LrtA was suggested by several pieces of evidence: (i) the lack of dispersion in NMR spectra (Figure 1); (ii) the shape (Figure 2A) and the deconvolution of far-UV CD spectrum; (iii) the absence of all-or-none co-operative transitions in the thermal and chemical denaturations (Figure 2B,C); and (iv) a model of the structure without the His-tag obtained with MD simulation (Figure 3).
Protein: DP02105 (UniProt P74518)
Region: residues 102	to 191
Annotation: disorder (Structural state)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
The intrinsically disordered nature of C-LrtA was suggested by several pieces of evidence: (i) the lack of dispersion in NMR spectra (Figure 1); (ii) the shape (Figure 2A) and the deconvolution of far-UV CD spectrum; (iii) the absence of all-or-none co-operative transitions in the thermal and chemical denaturations (Figure 2B,C); and (iv) a model of the structure without the His-tag obtained with MD simulation (Figure 3).
Protein: DP02105 (UniProt P74518)
Region: residues 102	to 191
Annotation: protein homodimerization activity (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The experiments with C-LrtA indicate a Rg ≈ 26 Å with a υ ≈ 0.33, close to a compact species value, but with a value of Rg larger than that of a well-folded protein (Section 4, Figure 4C), which is within the range observed for unfolded polypeptide chains [27]. We obtained a good agreement with the expected Guinier regime at low Q values, indicating that, although the protein was self-associated, the size of the C-LrtA species was relatively small.
Protein: DP02105 (UniProt P74518)
Region: residues 102	to 191
Annotation: protein homodimerization activity (Molecular function)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The protein species in the fastest migrating band corresponded to an apparent molecular weight of 33 kDa (close to the molecular weight of a dimer, and similar to that observed at the most diluted protein concentration in the SEC experiments). On the other hand, the other band corresponded to an apparent molecular weight of 66 kDa, denoting a pentamer. Our results also suggest that increasing the amount of SDS (well-below the concentration used in denaturing SDS-PAGE gels: 33 mM [28]) had significant effects on the population of self-associated C-LrtA species: the larger the proportion of SDS, the higher the amount of self-associated species detected (the critic micellar concentration of SDS is 1.33 mM).
Protein: DP02109 (UniProt O94316)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Thus, the NMR analysis confirms  both the computational and CD analyses that the Cwf10 NTE contains regions of disorder, most likely in the first 60 amino acids (Fig. 6A).
Protein: DP02118 (UniProt P19836)
Region: residues 1	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure at 2.2 Å resolution shows electron density for 353 residues of the possible 472 residues comprising the homodimer, with two bound CDP-choline molecules and 249 solvent molecules (Fig. 3A). Electron density is lacking for the N and C termini of both chains. Chain A accounts for residues 40–215 and chain B for residues 40–216. The crystal packing contacts allow sufficient space between adjacent stacked dimers to accommodate both N- and C-terminal regions as a disordered array.
Cross-references: PDB:3HL4
Protein: DP02118 (UniProt P19836)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Arg-C generated immediate cleavage at Arg12 and Arg14 in both CCTsol and CCTmem, showing for the first time that the N-terminal 15 residues of CCT are not a part of a compact fold (Fig. 8).
Protein: DP02118 (UniProt P19836)
Region: residues 217	to 236
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure at 2.2 Å resolution shows electron density for 353 residues of the possible 472 residues comprising the homodimer, with two bound CDP-choline molecules and 249 solvent molecules (Fig. 3A). Electron density is lacking for the N and C termini of both chains. Chain A accounts for residues 40–215 and chain B for residues 40–216. The crystal packing contacts allow sufficient space between adjacent stacked dimers to accommodate both N- and C-terminal regions as a disordered array.
Cross-references: PDB:3HL4
Protein: DP02118 (UniProt P19836)
Region: residues 237	to 293
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of domain M peptide in buffer or in the presence of OG were typical for predominantly random coil conformation as seen by the single negative maximum at 200 nm (Figure 6).
Protein: DP02118 (UniProt P19836)
Region: residues 294	to 312
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Each AI helix interacts with both αE helices, and together they form an antiparallel four-helix bundle near the opening of the active site. The two AI segments have very similar conformations with a bend at Lys281. AI-2 is unraveled between residues Gln276 and Trp278. Each AI helix ends in a sharp turn at 294GP (the AI-turn), which interacts with loop L2 at the mouth of the active site (discussed below).
The initial solution for the CCT-312 diffraction set was obtained using CCT-236 structure (Protein Data Bank code 3HL4) as a search model. Subsequent to the solution of the 3-Å CCT-312(Δ32) structure (Protein Data Bank code 4MVC), it was used as the search model for the 8-Å data set for CCT-312, which afforded a better fit to the experimental density.
Cross-references: PDB:4MVD
Protein: DP02118 (UniProt P19836)
Region: residues 311	to 367
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Thus chymotrypsin digestion proceeds from the more accessible C terminus, which was predicted to be loosely folded. The 42-kDa band is not quantitatively converted into the lower molecular mass fragments. This is likely because progressive removal of the C terminus results in increased protease sensitivity of the N-terminal domain. The molecular mass determinations for each fragment are considered accurate to within 1 kDa. Given this error factor there are actually three possible cleavage sites for the 35-kDa fragment: Leu-299, Leu-303, and Leu-311.
Protein: DP02118 (UniProt P19836)
Region: residues 313	to 367
Annotation: phosphorylation display site (Disorder function)
Evidence: radioisotope quantification assay evidence used in manual assertion
Supporting statements:
CT was the major phosphoprotein visible in the COS cell extracts (Figure 3). The amount of 32P associated with the CT band decreased with progressive deletion of the C-terminus (Figure 3). The radioactivity associated with each CT band was examined using four separate gels from two independent labelling experiments. Substitution of Ser-362 with alanine resulted in a 21 + 60'/ reduction in label; deletion of the
C-terminal 18 or 31 amino acids yielded a 26 + 14 % or 41 + 6%h reduction in 32P label respectively, and deletion of the C-terminal 55 amino acids eliminated all 32p label. This result suggests that the C-terminal 55 amino acids constitute the sole phosphorylation domain in CT and that there are multiple sites of phosphorylation.
Protein: DP02118 (UniProt P19836)
Region: residues 237	to 293
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of domain M peptide in buffer or in the presence of OG were typical for predominantly random coil conformation as seen by the single negative maximum at 200 nm (Figure 6). However, in the presence of LPC/PG micelles, or vesicles of PC/OA or PG, the CD spectra were characteristic of α-helices (strong positive band at ∼195 nm; strong minima at ∼208 and ∼222 nm).
Protein: DP02118 (UniProt P19836)
Region: residues 237	to 293
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of domain M peptide in buffer or in the presence of OG were typical for predominantly random coil conformation as seen by the single negative maximum at 200 nm (Figure 6). However, in the presence of LPC/PG micelles, or vesicles of PC/OA or PG, the CD spectra were characteristic of α-helices (strong positive band at ∼195 nm; strong minima at ∼208 and ∼222 nm).
The three activating lipid systems increased the α-helix content to a similar level of about 80% at the expense of β-strand, turn, and unordered, and nearly eliminated the β character from the spectra.
Protein: DP02118 (UniProt P19836)
Region: residues 238	to 299
Annotation: choline-phosphate cytidylyltransferase activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The activities of the C-terminal mutants are shown in Table 1. Neither substitution of Ser-362 with alanine nor deletion of the final 18, 31 or 55 residues had an effect on the activity of CT in the presence or absence of activating vesicles (PC: oleic acid, 1: 1) using a standard assay [45]. These mutants all contain the complete amphipathic helix domain of CT (see Figure 1) and were stimulated 3-4-fold by anionic lipid vesicles (Table 1). On the other hand, the mutant missing the last 140 amino acids, including the amphipathic helix and eight residues of the conserved domain, had less than 10 % of the catalytic activity of the wild type in the presence of PC-oleic acid vesicles. T
Domain M, but not domain P, is required for enzyme activity, lipid responsiveness and lntracellular localization
Protein: DP02118 (UniProt P19836)
Region: residues 238	to 299
Annotation: localization (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The subcellular distribution of the A228 mutant was altered. Whereas the other mutants were distributed, according to activity measurements, in approximately the same manner as the wildtype CT (63 + 3 %, cytosol; 15 + 3 %, microsomes; 22 + 7 %, low speed pellet), less than 3 % of the A228 mutant activity was in the microsomal fraction. This result was confirmed when we used digitonin permeabilization to assess the intracellular distribution. In cells transfected with wild-type CT or any of the mutants other than A228, 60-70 % of the CT activity was found in the cell lysate (soluble or cytosolic fraction). On the other hand 86 % of the A228 activity was associated with the lysate (Table 1).

Domain M, but not domain P, is required for enzyme activity, lipid responsiveness and lntracellular localization
Protein: DP02118 (UniProt P19836)
Region: residues 271	to 293
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Upon loss of the segment between residues 312 and 271, kcat values for the CCT soluble form transitioned from silenced (0.5 s−1) to the partially active rate (∼ 3 s−1) characteristic of CCT-236 (Fig. 1B). The construct ending at residue 271 showed a higher kcat than did CCT-255 or CCT-236, perhaps reflecting different consequences of specific truncation sites on protein dynamics. Loss of the AI segment was linked to a transition in the CTP Km from ∼9 to ∼5.5 mm (Fig. 1C). Thus, the presence of the AI segment suppresses kcat/Km by about 10-fold. However, the kinetic parameters of the full-length soluble enzyme were achieved only when the segment between residues 293 and 312 was intact. These results strengthen previous results implicating a key silencing role for the AI motif (16) but suggest additional participation of the flanking segment between residues 293 and 312.
Protein: DP02118 (UniProt P19836)
Region: residues 275	to 295
Annotation: self-assembly (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
A CCT-312(Δ32) crystal generated a 3-Å resolution diffraction data set that was solved by molecular replacement using CCT-236 (Protein Data Bank code 3HL4) (see Table 1). The asymmetric unit was a dimer. The resolved portion of this dimer encompasses the catalytic domains and the AI segments of domain M (Fig. 3A).
Each AI helix interacts with both αE helices, and together they form an antiparallel four-helix bundle near the opening of the active site.
The AI positioning in the CCT-312(Δ32) structure is not an artifact of the large domain M deletion. A very similar AI-αE-L2 interaction is found in CCT-312 with no deletion.
Cross-references: PDB:4MVC
Protein: DP02118 (UniProt P19836)
Region: residues 312	to 367
Annotation: disorder (Structural state)
Evidence: cleavage arrested development evidence used in manual assertion
Supporting statements:
The PBAMs reveal that domain P in both CCT forms was highly accessible to both chymotrypsin and Arg-C.
Protein: DP02118 (UniProt P19836)
Region: residues 312	to 367
Annotation: phosphorylation display site (Disorder function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
For the peptide spanning the entire domain P, Gln312-Asp367, the masses matched for four, five, six, and seven phosphates. Our analysis did not enable identification of each phosphorylated site; however, the results (Table II) indicate a phosphorylation pattern that is very similar to that obtained by MacDonald and Kent (12). The phosphorylated serines are spread over the entire 50-residue domain.
Protein: DP02118 (UniProt P19836)
Region: residues 36	to 69
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The low mass peptide data contributing to the PBAMs shown in Fig. 6 revealed enhanced accessibility of amino acids 41 and 59 in domain N of CCTmem and CCT236 (region II).
Two other important differences between CCTsol and CCTmem, evidenced from chymotrypsin digestion, were also revealed by Arg-C digestion: (i) Sites within domain N at Arg36, Arg42, Arg61, and Arg69 were cleaved to generate a variety of peptides in CCTmem, whereas none of these sites were cleaved in CCTsol for at least 10 min of digestion (Fig. 6C and Supplementary Fig. 1C). Thus the limited digestion pattern generated by two different proteases indicate that membrane binding increases the accessibility of the C-terminal side of domain N (Fig. 6, region II).
Because membrane binding exposes a region of domain N, but not domain C, we hypothesize that in the soluble form domain M of CCT interacts with the region of domain N that becomes exposed upon membrane binding of domain M.
Protein: DP02118 (UniProt P19836)
Region: residues 36	to 69
Annotation: order to disorder (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The low mass peptide data contributing to the PBAMs shown in Fig. 6 revealed enhanced accessibility of amino acids 41 and 59 in domain N of CCTmem and CCT236 (region II).
Two other important differences between CCTsol and CCTmem, evidenced from chymotrypsin digestion, were also revealed by Arg-C digestion: (i) Sites within domain N at Arg36, Arg42, Arg61, and Arg69 were cleaved to generate a variety of peptides in CCTmem, whereas none of these sites were cleaved in CCTsol for at least 10 min of digestion (Fig. 6C and Supplementary Fig. 1C). Thus the limited digestion pattern generated by two different proteases indicate that membrane binding increases the accessibility of the C-terminal side of domain N (Fig. 6, region II).
Because membrane binding exposes a region of domain N, but not domain C, we hypothesize that in the soluble form domain M of CCT interacts with the region of domain N that becomes exposed upon membrane binding of domain M.
Protein: DP02118 (UniProt P19836)
Region: residues 36	to 69
Annotation: order (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Two other important differences between CCTsol and CCTmem, evidenced from chymotrypsin digestion, were also revealed by Arg-C digestion: (i) Sites within domain N at Arg36, Arg42, Arg61, and Arg69 were cleaved to generate a variety of peptides in CCTmem, whereas none of these sites were cleaved in CCTsol for at least 10 min of digestion (Fig. 6C and Supplementary Fig. 1C). Thus the limited digestion pattern generated by two different proteases indicate that membrane binding increases the accessibility of the C-terminal side of domain N (Fig. 6, region II).
Protein: DP02118 (UniProt P19836)
Region: residues 237	to 293
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectra of domain M peptide in buffer or in the presence of OG were typical for predominantly random coil conformation as seen by the single negative maximum at 200 nm (Figure 6). However, in the presence of LPC/PG micelles, or vesicles of PC/OA or PG, the CD spectra were characteristic of α-helices (strong positive band at ∼195 nm; strong minima at ∼208 and ∼222 nm).
Protein: DP02120 (UniProt Q00944)
Region: residues 363	to 393
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino-terminal portion of the linker—including the Src SH3 docking site—is disordered in the present structure (residues 363–393)
Cross-references: PDB:2J0K
Protein: DP02120 (UniProt Q00944)
Region: residues 573	to 584
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The kinase activation loop adopts an inactive conformation in which it extends toward the FERM domain (near Ser46 in the F1 lobe) and is then unstructured between residues Asp573 and Leu584.
Cross-references: PDB:2J0K
Protein: DP02122 (UniProt Q02199)
Region: residues 121	to 154
Annotation: disorder (Structural state)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
This fragment is demonstrated to be intrinsically disordered by smFRET as well as by SAXS measurements
Protein: DP02122 (UniProt Q02199)
Region: residues 121	to 154
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
This fragment is demonstrated to be intrinsically disordered by smFRET as well as by SAXS measurements
Cross-references: SASBDB:SASDEH2
Protein: DP02122 (UniProt Q02199)
Region: residues 1	to 269
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Cryo-EM structure of the Inner spoke ring of the yeast NPC shows this region of the NUP49 protein lacks electron density, indicating it is disordered. 
Cross-references: PDB:8TJ5
Protein: DP02122 (UniProt Q02199)
Region: residues 408	to 428
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Cryo-EM structure of the Inner spoke ring of the yeast NPC shows this region of the NUP49 protein lacks electron density, indicating it is disordered. 
Cross-references: PDB:8TJ5
Protein: DP02122 (UniProt Q02199)
Region: residues 1	to 260
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: thioflavin T based fluorescence spectroscopy evidence
Supporting statements:
The ThT assay reported dramatically fastened amyloid formation kinetics of hNup153FG in buffer containing serine. Increasing serine concentrations even led to instantaneous aggregation of the protein (Fig 1A).
A similar phenomenon was observed for yNup49FG (supplementary Fig S1 online), indicating that also crowding-induced aggregation might be a common property of FG Nups and conserved across species.
Amyloid formation proceeded readily at 28°C under agitation.
Protein: DP02122 (UniProt Q02199)
Region: residues 1	to 260
Annotation: molecular condensate scaffold activity (Molecular function)
Evidence: fluorescence resonance energy transfer evidence used in manual assertion
Supporting statements:
This aggregation occurred even at the single-molecule level (pM protein concentrations, see Fig 1F; supplementary Fig S2 online) and is thus extremely high under molecular crowding conditions. As enhanced aggregation also occurred in the presence of other cosolutes such as lysine, trimethylaminoxid and the large molecule polyethylene glycol 20,000, we conclude that the aggregation accelerating effect is not owing to a specific chemical functionality but rather a general phenomenon, like space restriction or sequestering of water.
A similar phenomenon was observed for yNup49FG (supplementary Fig S1 online), indicating that also crowding-induced aggregation might be a common property of FG Nups and conserved across species.