LiteFold/DisProt huggingface dataset:
Protein: DP03969 (UniProt Q9H1A4)
Region: residues 1933	to 1944
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the human Anaphase-promoting complex/Cyclosome with E2 UBE2S and UBE2C shows this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:5L9U
PDB:5L9T
EMDB:3432
EMDB:3433
Protein: DP03970 (UniProt Q9NW15)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model encompasses all residues from Ser13-Lys641 and three Ca2+ ions per monomer (Supplementary Table 3).
Cross-references: PDB:6R7Y
PDB:6R7Z
PDB:6R7X
PDB:6R65
EMDB:4746
EMDB:4747
EMDB:4748
Protein: DP03970 (UniProt Q9NW15)
Region: residues 642	to 660
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model encompasses all residues from Ser13-Lys641 and three Ca2+ ions per monomer (Supplementary Table 3).
Cross-references: PDB:6R7Y
PDB:6R7Z
PDB:6R7X
PDB:6R65
EMDB:4746
EMDB:4747
EMDB:4748
Protein: DP03970 (UniProt Q9NW15)
Region: residues 463	to 474
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cytoplasmic α7−α8 region was poorly resolved and truncated between residues 463–474.
Cross-references: PDB:6R7Z
EMDB:4748
Protein: DP03970 (UniProt Q9NW15)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final LCP model encompasses residues Ser14 to Gln639.
Cross-references: PDB:5OC9
Protein: DP03970 (UniProt Q9NW15)
Region: residues 640	to 660
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final LCP model encompasses residues Ser14 to Gln639.
Cross-references: PDB:5OC9
Protein: DP03971 (UniProt Q10567)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7R4H
Protein: DP03972 (UniProt Q62768)
Region: residues 1341	to 1351
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Some of the loops connecting the helices did not yield interpretable electron density, suggesting that they are disordered. 
Cross-references: PDB:3SWH
Protein: DP03972 (UniProt Q62768)
Region: residues 1458	to 1467
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Some of the loops connecting the helices did not yield interpretable electron density, suggesting that they are disordered. 
Cross-references: PDB:3SWH
Protein: DP03972 (UniProt Q62768)
Region: residues 1517	to 1531
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues, by chain A: 1148-1155, 1341-1351, 1459-1468, 1515-1531
B: 1148-1155, 1341-1351, 1458-1467, 1517-1531
Cross-references: PDB:3SWH
Protein: DP03973 (UniProt P33891)
Region: residues 217	to 234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model (Supplementary Fig. 3) spans nearly the entire molecule, comprising residues 5-701, with residues 217-234 and 546-551 missing because of disordered loops that are not visible in any electron density map.
Cross-references: PDB:3FHN
Protein: DP03974 (UniProt P53847)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We were able to produce soluble full-length yeast Dsl1p (residues 1-754), but could not generate diffraction-quality crystals, perhaps because the full-length protein contains a central region (residues 388-467) with an unusual concentration of charged residues28 and an absence of predicted regular secondary structure.
No electron density was discernable for the first 36 residues of Dsl1ΔC, suggesting that the extreme N-terminus, while present, is not crystallographically well ordered.
Cross-references: PDB:3ETU
Protein: DP03974 (UniProt P53847)
Region: residues 388	to 467
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We were able to produce soluble full-length yeast Dsl1p (residues 1-754), but could not generate diffraction-quality crystals, perhaps because the full-length protein contains a central region (residues 388-467) with an unusual concentration of charged residues28 and an absence of predicted regular secondary structure.
Cross-references: PDB:3ETU
Protein: DP03975 (UniProt P14867)
Region: residues 351	to 410
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins were not included.
Intracellular domains (ICD), largely disordered in the absence of interacting post-synaptic proteins, could only be partially modelled (Extended Data Fig. 3m, Supplementary Video 2).
Cross-references: PDB:6I53
EMDB:EMD-4411
Protein: DP03976 (UniProt P28472)
Region: residues 338	to 439
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins were not included.
Intracellular domains (ICD), largely disordered in the absence of interacting post-synaptic proteins, could only be partially modelled (Extended Data Fig. 3m, Supplementary Video 2).
Cross-references: PDB:6I53
EMDB:EMD-4411
Protein: DP03977 (UniProt P18507)
Region: residues 363	to 444
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins were not included.
Intracellular domains (ICD), largely disordered in the absence of interacting post-synaptic proteins, could only be partially modelled (Extended Data Fig. 3m, Supplementary Video 2).
Cross-references: PDB:6I53
EMDB:EMD-4411
Protein: DP03977 (UniProt P18507)
Region: residues 1	to 65
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the the CRYO EM structure, indicating it is disordered.
Cross-references: PDB:6I53
Protein: DP03978 (UniProt P19658)
Region: residues 222	to 233
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure consists of residues 67–623 (with the exception of residues in disordered regions 117–120, 222–233, 296–300 and 415–418) and 261 water molecules.
Cross-references: PDB:2B1E
Protein: DP03979 (UniProt F2SDI0)
Region: residues 585	to 815
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
However, PacCΔ1−584, with a predicted Mw of 24.7 kDa, exhibited an anomalous migration on SDS-PAGE of ∼35 kDa, possibly due to the enrichment of charged residues in these proteins, as also observed in many IDPs.
Protein: DP03979 (UniProt F2SDI0)
Region: residues 585	to 815
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Size-exclusion chromatography (SEC) of PacCΔ1−584 was next performed to estimate its hydrodynamic properties. Again, although the protein eluted as one major peak over the Superdex 200 10/300 GL column, the apparent Mw was found to be ∼five-fold higher than that of the monomer, that is, 126 ± 0.88 kDa (Figure 3A). A nearly four- to six-fold increase in their apparent Mw is often seen for IDPs
having an extended random coil conformation, suggesting a possible similar conformation for PacCΔ1−584 as well.
Protein: DP03979 (UniProt F2SDI0)
Region: residues 585	to 815
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In order to monitor the secondary structure of PacCΔ1−584, far-UV CD spectrum was recorded at alkaline ambient pH 8.0 (Figure 4A). The CD spectrum shows a negative peak at 200 nm, similar to the spectrum shown by intrinsically disordered proteins.
Protein: DP03979 (UniProt F2SDI0)
Region: residues 585	to 815
Annotation: disorder (Structural state)
Evidence: intrinsic fluorescence-based protein conformation evidence
Supporting statements:
The intrinsic fluorescence spectrum of PacCΔ1−584 is suggestive of a fully exposed environment for tryptophan between pH 2 and 12, with λmax of 355−357 nm
(Figure S2), limiting the estimation of thermodynamic parameters to far-UV CD measurements.
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
IDPRs characteristically demonstrate slow migration in SDS-polyacrylamide gels due to their expanded nature and greater number of charged residues which leads to weak binding to SDS (26, 43). Full-length WT CLEC16A and the CLEC16A ΔIDPR mutant migrated at their expected molecular mass (Fig. 6A). However, the internal CLEC16A putative IDPR alone (AA 347–472) migrated a shorter distance than what is expected, visualized as a band 1.6-times greater than the expected size, consistent with an IDPR (Fig. 6A).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Notably, the heteronuclear single quantum coherence-NMR spectra of the CLEC16A putative internal IDPR was tightly clustered near 8 ppm, supporting the hypothesis that CLEC16A contains an internal IDPR (Fig. 6B).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Conversely, the CD spectra of the putative internal CLEC16A IDPR had a single minimum near 200 nm, in line with lack of secondary structure (Fig. 6D).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: disorder (Structural state)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
Further, while heating full-length CLEC16A irreversibly disrupted its alpha-helical secondary structure, heating the internal CLEC16A fragment did not substantially change its spectral features (Fig. 6, C and D). This result confirmed that the internal CLEC16A fragment lacks secondary structure and is indeed an IDPR (Fig. 6, C and D).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: protein binding (Molecular function)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
We find that the internal IDPR of CLEC16A is crucial for its degradation. CLEC16A turnover was promoted by RNF41, which binds and acts upon the internal IDPR to destabilize CLEC16A.
Truncating the CLEC16A internal IDPR, or shuffling its residues, reduced CLEC16A binding and ubiquitination of RNF41 compared to WT CLEC16A, following overexpression of the similar protein levels of CLEC16A (Fig. 5A). Mutating the CLEC16A internal IDPR also impaired assembly of the tripartite mitophagy complex, as we found reduced binding between CLEC16A and RNF41 as well as RNF41 and USP8 (Fig. 5B).
Indeed, overexpression of the CLEC16A internal IDPR fragment alone (AA 347–472; IDPR1 only) was sufficient to bind RNF41 (Fig. 5C).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: regulation of proteasomal ubiquitin-dependent protein catabolic process (Biological process)
Evidence: immunoprecipitation evidence used in manual assertion
Supporting statements:
We found that the CLEC16A internal IDPR contains an enrichment of lysine residues that are predicted to be ubiquitinated with high confidence (Fig. 2D). We therefore generated a CLEC16A mutant construct insensitive to ubiquitination with lysine-to-arginine mutagenesis of the internal IDPR (IDPR K-to-R), which is a substitution strategy that retains a similar residue structure and charge. The CLEC16A IDPR K-to-R mutant had increased protein levels and was significantly more stable than WT CLEC16A and achieved similar levels and stability to CLEC16A mutants bearing a shuffled or truncated internal IDPR (Fig. 2, E and F).
Interestingly, the CLEC16A mutant lacking the internal IDPR maintained higher protein levels and was more stable than WT CLEC16A, indicating that the internal IDPR destabilized CLEC16A (Fig. 2C).
While overexpressing RNF41 led to reduced levels of WT CLEC16A as expected, shuffling or truncating the internal IDPR prevented RNF41 from reducing CLEC16A protein levels (Fig. 4D). Further, overexpression of a dominant negative RNF41 lacking its RING domain (dnRNF41) to inhibit RNF41 action led to an elevation in the levels of WT CLEC16A, but this did not occur following truncation of the internal IDPR (Fig. 4E). These results suggest that RNF41 acts upon the CLEC16A internal IDPR to destabilize CLEC16A and that this action depends upon the CLEC16A IDPR amino acid sequence order.
Moreover, RNF41 also did not reduce levels of the ubiquitination-resistant CLEC16A
internal IDPR mutant (IDPR K-to-R), suggesting that CLEC16A internal IDPR lysine residues are vital for RNF41 to destabilize CLEC16A (Fig. 4D).
Protein: DP03980 (UniProt Q80U30-3)
Region: residues 347	to 472
Annotation: protein destabilization (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
Interestingly, the CLEC16A mutant lacking the internal IDPR maintained higher protein levels and was more stable than WT CLEC16A, indicating that the internal IDPR destabilized CLEC16A (Fig. 2C).
Protein: DP03982 (UniProt Q7Y1A0)
Region: residues 1	to 210
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous buffers, the spectrum of the proteins in the far-UV region (190–250 nm) exhibited a strong negative band at ~199 nm, and weak negative ellipticity at 222 nm, which indicated that the proteins were predominantly in a random coil conformation, lacking a well-defined secondary structure (Fig. 5A–D).
Protein: DP03982 (UniProt Q7Y1A0)
Region: residues 1	to 210
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Since a large number of unfolded proteins undergo induced folding upon interactions with their binding partner, the intrinsic propensity of the analyzed proteins to adopt α-helical structures was examined in the presence of negatively charged SDS micelles that have previously been used to model the lipoprotein environment (Rozek et al., 1995, Tulumello and Deber, 2009). Upon incubation with SDS, DHN24 exhibited a pronounced increase in its helical content (Fig. 5A). The negative band shifted from 199 to 204 nm. The CD spectra also contained a stronger negative shoulder at 208–222 nm and positive bands at 190–192 nm, which were characteristics of α-helical structures.
Protein: DP03982 (UniProt Q7Y1A0)
Region: residues 1	to 210
Annotation: phospholipid binding (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Since dehydrins can bind to acidic phospholipids (Kovacs et al., 2008; Koag et al., 2009; Clarke et al., 2015), it was examined whether the cationic nature of the lysine-rich segments of DHN24 could modulate potential interactions with negatively charged phospholipids. Before the examination, immunoblot analysis was performed using polyclonal anti-DHN24 antibodies to assess the quality of the detected signal of recombinant DHN24 and its mutant variants: dM1, dsM2, and dsM3. The antibodies detected all the proteins with similar affinity (Fig. 7A). Mutant proteins exhibited a slower migration in SDS-PAGE than DHN24 which may be due to the lower content of lysine residues, possibly reducing association with negatively charged SDS
Protein: DP03982 (UniProt Q7Y1A0)
Region: residues 1	to 210
Annotation: phospholipid binding (Molecular function)
Evidence: in vitro assay evidence used in manual assertion
Supporting statements:
After the experiments, lipid-protein interaction assays were performed. Anionic PA was immobilized on a nitrocellulose membrane along with neutral phospholipid LPC since zwitterionic lipids are less attracted to dehydrins (Koag et al., 2009; Clarke et al., 2015). DHN24 and dM1 were found to bind to PA upon incubation, but binding to LPC was very weak (Fig. 7B).
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 21	to 143
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Resonances are dispersed in a narrow spectral range from 8 to 8.7 ppm, which is the hallmark of an intrinsically disordered protein.14 The observed chemical shifts result from the average of a conformational ensemble the protein may adopt if the exchange time scale is much faster than the chemical shift time
scale.
The N- and C-termini present highly negative hetNOE values indicating high flexibility.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 21	to 143
Annotation: disorder to order (Structural transition)
Evidence: high throughput mass spectrometry evidence used in manual assertion
Supporting statements:
Along this line, the HRMS observation suggests that silver-bound SilE is generally less disordered than silver-free SilE, which is consistent with the NMR and CD
data.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 110	to 122
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, we have detected measurable shifts in the regions H80 to M90 and M59 to M72 before the signal disappearance where 3 HxxM and 1 MxxH motifs are present.
Large variations of CSP are observed for residues E110 to N122 and residues H129 to S141.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 110	to 123
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure propensities15 calculated from the backbone chemical shift assignment for each residue of the silver-bound SilE in the presence of 6 equivalents of Ag+ in solution further confirmed the α-helix folding upon silver addition (Fig. 4(B)). The folded area encompasses more residues compared to the free form (segments 110–123 + 128–142 vs. 112–117 + 132–139 without silver) and the α-helix propensity increases from 18% in the free state up to 65% in the bound state.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 128	to 142
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure propensities15 calculated from the backbone chemical shift assignment for each residue of the silver-bound SilE in the presence of 6 equivalents of Ag+ in solution further confirmed the α-helix folding upon silver addition (Fig. 4(B)). The folded area encompasses more residues compared to the free form (segments 110–123 + 128–142 vs. 112–117 + 132–139 without silver) and the α-helix propensity increases from 18% in the free state up to 65% in the bound state.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 57	to 95
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
A series of CD experiments were performed and confirmed the formation of α-helix upon silver binding for this shorter construct (Fig. S6, ESI†) as observed for the full-length SilE.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 21	to 143
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Through the Guinier plot analysis, we derived a radius of gyration Rg = 37.7 ± 0.7 Å for free SilE and Rg = 32.9 ± 0.2 Å for SilE + 6 equivalents Ag+. Therefore, we can conclude the compactness of the structure in the presence of silver as observed in IM-MS experiments.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 80	to 90
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, we have detected measurable shifts in the regions H80 to M90 and M59 to M72 before the signal disappearance where 3 HxxM and 1 MxxH motifs are present.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 59	to 72
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, we have detected measurable shifts in the regions H80 to M90 and M59 to M72 before the signal disappearance where 3 HxxM and 1 MxxH motifs are present.
Protein: DP03984 (UniProt Q9Z4N3)
Region: residues 129	to 141
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additionally, we have detected measurable shifts in the regions H80 to M90 and M59 to M72 before the signal disappearance where 3 HxxM and 1 MxxH motifs are present.
Protein: DP03985 (UniProt Q922S8)
Region: residues 183	to 223
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The distal half of the neck, Ser183–Phe223, is predicted to form a helical structure, but this region was disordered and it was not possible to trace. 
Cross-references: PDB:1V8J
Protein: DP03988 (UniProt Q86WX3)
Region: residues 1	to 136
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
For a more detailed structural analysis of AROS, we then performed 2D-NMR spectroscopy. The [1H,15N]-HSQC spectrum of AROS (Figure 2E) displays poor signal dispersion in the 1H dimension, indicating that AROS lacks a stable and complete tertiary structure in absence of relevant factors such as an interaction partner or crowding environment.