LiteFold/DisProt huggingface dataset:
Protein: DP03659 (UniProt Q14318)
Region: residues 1	to 32
Annotation: self-inhibition (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
As seen in Table 1, consistent with a previous study8, the isomerase activity of the full-length FKBP38 was activated by the addition of CaM/Ca2+. Interestingly, the FKBD38 showed similar levels of PPIase activity in the absence of CaM/Ca2+, suggesting that either the N- or C-terminal extensions were inhibitory and responsive to CaM/Ca2+. We then identified that NTD, a fragment of FKBP38, containing the N-terminal extension, but lacking the C-terminal extension, was activated by the addition of CaM/Ca2+ (Table 1). Taken together, the data suggest that the core isomerase activity of FKBP38 is inhibited by the N-terminal extension residues flanking the isomerase domain and that this inhibition is overcome by the addition of CaM/Ca2+.
The core isomerase activity of FKBP38 is inhibited by transient interactions involving the flexible N-terminal extension that precedes the catalytic domain.
Protein: DP03659 (UniProt Q14318)
Region: residues 1	to 34
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, this FKBP381–165 variant showed a considerably higher stability in the presence of Ca2q-CaM compared to FKBP3835–153, but the 1 H/15N-HSQC spectra were dominated by a large number of very strong amide signals with narrow line-width that belong to the evidently non-structured segments Met1-Glu34 and Asp151-Asn165.
Protein: DP03659 (UniProt Q14318)
Region: residues 151	to 165
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, this FKBP381–165 variant showed a considerably higher stability in the presence of Ca2q-CaM compared to FKBP3835–153, but the 1 H/15N-HSQC spectra were dominated by a large number of very strong amide signals with narrow line-width that belong to the evidently non-structured segments Met1-Glu34 and Asp151-Asn165.
Protein: DP03659 (UniProt Q14318)
Region: residues 1	to 34
Annotation: calmodulin binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the reverse experiment, upon titration with Ca2q-CaM strong CSP as well as line-broadening effects were observed at the Glu-rich N-terminus of 15N-labeled FKBP381–165 (Figure 4D), in particular within the segment Ala9-Glu26. The line-broadening effects, which were most pronounced for residues Leu15, Arg17, Leu20, Ala22, Met23 and Glu24, imply that this non-structured Glu-rich region interacts directly with CaM, or more precisely with helix A of the N-terminal CaM lobe which had exhibited additional binding-related effects compared to the experiments with the shorter FKBP3835–153 variant (Figure 4C).
Interestingly, the CSP effects found for 15N-labeled Ca2qCaM in the presence of the FKBP381–165 variant are similarly strong as in the case of FKBP3835–153 (Figure 4C),
suggesting that the contribution of the FKBP38 segment Ala9-Glu26 to this protein-protein interaction is only of minor importance.
Protein: DP03659 (UniProt Q14318)
Region: residues 357	to 380
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The lack of electron density in this region, shown in the PDB, indicates an IDR.
Cross-references: PDB:5MGX
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: protein binding (Molecular function)
Evidence: peptide array evidence used in manual assertion
Supporting statements:
Using arrays of overlapping 20‐mer peptides of FKBP8 moved by increments of three amino acids to cover the full‐length sequence, we detected a single LIR motif in the N‐terminus with the core sequence FEVL (Fig 1B).
Taken together, these results allowed the conclusion that FKBP8 contains a canonical N‐terminal LIR motif that interacts preferentially with LC3A in vivo.
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Mutations in the core LIR motif resulted in a significantly reduced FKBP8 binding to the ATG8 proteins (Fig 1C and D). Quantitation of the FKBP8 interactions shows high‐affinity binding toward GABARAPL1 and LC3A (Fig 1D), low‐affinity binding toward GABARAPL2 and LC3C, and intermediary‐affinity binding toward LC3B and GABARAP.
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
To investigate whether FKBP8 interacts with the ATG8 homologs in vivo, GFP‐tagged ATG8 proteins were co‐expressed with Flag‐tagged wild‐type (WT) or LIR‐mutated FKBP8 in HeLa cells, before immunoprecipitations using a Flag antibody. Efficient co‐precipitation of LC3A, and a weaker but significant co‐precipitation of LC3B were observed (Fig 1E). Surprisingly, only moderate co‐precipitation of GABARAP and no co‐precipitations of GABARAPL1 and GABARAPL2 were detected (Fig 1E). Consistent with the in vitro data, the FKBP8 LIR mutant did not co‐precipitate any of the ATG8 homologs.
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: regulation of mitophagy (Biological process)
Evidence: co-localization evidence used in manual assertion
Supporting statements:
To investigate if the co‐localization of LC3A and FKBP8 is mediated by the FKBP8 LIR motif, a Cerulean‐FKBP8 LIR mutant (F24A/L27A, hereafter denoted LIRm) was co‐expressed with EYFP‐LC3A and mCherry‐OMP25TM in the HeLa cells. Strikingly, the FKBP8 LIRm is localized both on the mitochondria and on ER, but it fails completely to co‐localize with LC3A upon CCCP treatment (Fig 3A–C). Instead, LC3A forms visible aggregates that do not overlap with the mCherry‐OMP25TM probe (Fig 3A), similarly as the vector control (Fig EV3A). Together, these results suggest that CCCP treatment induces a LIR‐mediated interaction between FKBP8 and LC3A, and this interaction is important for mitochondrial recruitment of LC3A.
Taken together, our results show that FKBP8 mediates LIR‐dependent recruitment of LC3A to damaged mitochondria.
Importantly, the mitochondrial acidification was LIR dependent, and enhanced when FKBP8 was specifically targeted to the mitochondria (Fig 5B).
We find here that FKBP8 promotes mitophagy by LIR‐dependent recruitment of LC3A, independent of the PINK1‐Parkin pathway.
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: regulation of mitophagy (Biological process)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
These two FKBP8 mutants all showed an impaired ability to degrade mitochondria under normoxic and hypoxic conditions (Figure 5F,G,H).
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Expression analysis of those mutants revealed that FKBP8 LIR mutant failed to bind to GFP-LC3B and recruit it onto the mitochondria (Figure 5B,C), consistent with the previous report.
LIR motif coresponds to the 24-27 region.
Protein: DP03659 (UniProt Q14318)
Region: residues 23	to 28
Annotation: protein localization to mitochondrion (Biological process)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Expression analysis of those mutants revealed that FKBP8 LIR mutant failed to bind to GFP-LC3B and recruit it onto the mitochondria (Figure 5B,C), consistent with the previous report.
LIR motif coresponds to the 24-27 region.
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 1403	to 1430
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structural model contains most of residues from ankyrin-B ZZUD except for a few flexible loops (Fig. 1A)
Cross-references: PDB:4D8O
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 1403	to 1430
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structural model contains most of residues from ankyrin-B ZZUD except for a few flexible loops (Fig. 1A)
Cross-references: PDB:4D8O
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 1059	to 1068
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structural model contains most of residues from ankyrin-B ZZUD except for a few flexible loops (Fig. 1A)
Cross-references: PDB:4D8O
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 1059	to 1068
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structural model contains most of residues from ankyrin-B ZZUD except for a few flexible loops (Fig. 1A)
Cross-references: PDB:4D8O
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 796	to 852
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
IDR is 100% identical.
Cross-references: DisProt:DP03650r005
PDB:4RLV
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 662	to 672
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
IDR is 100% identical.
Cross-references: DisProt:DP03650r007
PDB:5Y4D
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 825	to 852
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
IDR is 100% identical.
Cross-references: DisProt:DP03650r006
PDB:5Y4F
Protein: DP03660 (UniProt A0A5F9ZHA1)
Region: residues 1189	to 1201
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
IDR is 100% identical.
Cross-references: DisProt:DP03650r008
PDB:6M3Q
Protein: DP03661 (UniProt Q9BY41)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered segments in the final model include M1-S13, E85-I94, and I378-H389 in monomer A, and M1-Q12, Q84-S93, and E379-H389 in monomer B.
Cross-references: PDB:3RQD
Protein: DP03662 (UniProt P0AB71)
Region: residues 178	to 194
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The model consists of three polypeptide segments, residues 1–176, 194–228 and 230–356. There is no convincing electron density for residues 177–193, 229 or the last two residues in the sequence.
We were never able to locate the remaining selenium, Met190, as it is located on a flexible loop.
The IDR characterized in the publication and spanning residues 177-193 corresponds to region 178-194 of the amino acid sequence, since the N-terminal methionine is removed from the protein.
Cross-references: PDB:1ZEN
Protein: DP03663 (UniProt P0A9I5)
Region: residues 76	to 87
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
No resonance assignments were obtained for residues 1, 2, 79, 80, and the C-terminal His tag residues 89–95 because of chemical exchange and flexibility of the N- and C-terminal parts of the NapD structure.
The final β-strand in the NapD fold (residues 69–75) was followed by a flexible, unstructured, carboxyl-terminal tail.
The residues that were least affected upon peptide binding were, in general, localized within the α-helical and turn regions (residues 53–69 and 17–31) on the opposite side of the molecule, or within the flexible C terminus, consistent with the peptide-binding site being located within the β-sheet.
Of residues 3–78 (backbone rmsd, 1.25 Å), the core region containing the secondary structure elements (residues 6–75) is well defined (backbone rmsd, 0.63 Å) and deemed suitable for detailed structural analysis (Table 1).
However, the C-terminally truncated NapD (DC-term), which is lacking the final 10 very flexible residues, was partially compromised in its physiological activity, suggesting that the unstructured C-tail may have role in NapD function.
Cross-references: BMRB:15381
PDB:2JSX
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Under native conditions and neutral pH, both spectra display a large negative peak centered at 200 nm, low intensity in the 220–230 nm region, and low ellipticity at 190 nm (Figure 8A). The spectra are typical of disordered proteins lacking any stable organized secondary structure. For both proteins, spectral deconvolution revealed a high content (about 60%) of unordered structure along with a ~20% content in β-strands (Figure 8B).
According to their ellipticity values at 200 and 222 nm, both W proteins fall in the PMG-like region of the plot (Figure 8C). These results confirm the hints obtained from SEC experiments and support the classification of the W proteins within the PMG-like sub-family of IDPs.
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The pairiwse distance distribution, P(r), yielded a maximal dimension, Dmax, of ~240 Å for HeV and ~245 Å for NiV W (Supplementary Figure S6C) with a long tail in the P(r) function, indicating that the proteins assume an overall non-compact conformation [69].
The flexible nature of the W proteins was also qualitatively assessed using the Kratky- Debye and the normalized Kratky plots (Figure 10C,D). The presence of a plateau in the Kratky-Debye plot (Figure 10C) and the shape of the normalized Kratky plot (with no clear maximum) (Figure 10D) indicate that the W proteins are intrinsically disordered.
For both proteins, the resulting final Rg (Figure 10E,F) and Dmax (Supplementary Figure S6D) distributions, are unimodal and close to those of the initial pool, indicating that the W proteins exist in solution as randomly distributed ensembles of non-compact and highly flexible conformations.
In conjunction with all the other experimental lines of evidence presented above, SAXS data definitely demonstrate that the W proteins are intrinsically disordered.
Cross-references: SASBDB:SASDLK9
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: pre-molten globule (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
From the elution volume of the major species (16.0 ± 0.08 mL for HeV W and 16.1 ± 0.07 mL for NiV W), as obtained using HBS as elution buffer, the corresponding RS was estimated to be 51.0±0.9Å for HeVW and 50.1±0.8Å for NiVW (Table2). By comparing the mean measured Stokes radius (Rsobs) for HeV and NiV W with the theoretical Stokes radii expected for various conformational states (RsNF: natively folded protein; RSPMG: expected for a PMG; RsU: fully unfolded form; RSIDP: expected for an IDP), the two proteins were found to have RS values ~1.7 times larger than the value expected for a natively folded protein, and close to the one expected for a PMG (Table 2). 
These results, while providing additional experimental evidence for the prevalently disordered nature of both W proteins, indicate the presence of some transiently populated secondary and/or tertiary structure typical of the PMG state, also supported by the expansion effect observed in the presence of urea.
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: disorder (Structural state)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
The experimentally observed profile obtained for both the W proteins does not feature any transition peak, consistent with the lack of a stable 3D structure (Figure 6). These results provide additional support for an overall disordered nature of the W proteins, in line with the in-silico analyses and with the above-described experimental lines of evidence.
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
As shown in Figure 5, both proteins start to be degraded after 5 minutes of incubation and are extensively degraded after 45 minutes, a behavior that is consistent with the lack of a packed core and with an overall solvent accessibility.
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
As shown in Figure 4A, B the final purified W proteins migrate with an apparent molecular mass of ~65 kDa, a value 1.2 times higher than the one expected from the amino acid sequence (~53 kDa).
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: amyloid fibril formation (Biological process)
Evidence: transmission electron microscopy evidence used in manual assertion
Supporting statements:
Finally, we analyzed the purified W proteins using negative-staining TEM, which unambiguously revealed the presence of fibrils for both HeV and NiV W (Figure 12).
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: response to leptomycin B (Biological process)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
As per V, the nuclear localization of HeV W also increased following LMB treatment (p < 0.0001) (Fig. 1a,b), but in contrast the localization of HeV P remained unchanged following LMB treatment (Fig. 1a,b). Thus, the nucleocytoplasmic localization of HeV V and W, but not P, is dependent on an exportin-1-dependent nuclear export sequence (NES).
Protein: DP03664 (UniProt P0C1C6)
Region: residues 1	to 448
Annotation: host cell nucleus (Cellular component)
Evidence: confocal laser scanning microscopy evidence used in manual assertion
Supporting statements:
In untreated cells, HeV P and V were excluded from the nucleus, whereas W showed strong nuclear localization, but was excluded from structures consistent with nucleoli (Fig. 1a,b).
Protein: DP03665 (UniProt P33734)
Region: residues 261	to 275
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two exposed loops in the C-terminal cyclase domain (residues 261–275 and 301–304) are disordered and were not modeled.
Cross-references: PDB:1JVN
Protein: DP03666 (UniProt Q12983)
Region: residues 146	to 158
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Broken lines separate the unfolded regions 146–158 and 188–190 from the α-helical regions 159–165, 166–184, and 185–187 regions that have different flexibility.
In contrast, the residues 146–158 and 188–190 from the N- and C termini, respectively, have nearly unrestricted mobility, resulting in low and negative 15N{1H} NOEs and decreased local rotation correlation times τR, estimated from the T1/T2 ratio (Fig. 3).
The residues 146-158 of the analized construct coresponds to the 211-223 region of the BCL2/adenovirus E1B 19 kDa protein-interacting protein 3.
Cross-references: PDB:2J5D
BMRB:7288
Protein: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Under native conditions and neutral pH, both spectra display a large negative peak centered at 200 nm, low intensity in the 220–230 nm region, and low ellipticity at 190 nm (Figure 8A). The spectra are typical of disordered proteins lacking any stable organized secondary structure. For both proteins, spectral deconvolution revealed a high content (about 60%) of unordered structure along with a ~20% content in β-strands (Figure 8B).
According to their ellipticity values at 200 and 222 nm, both W proteins fall in the PMG-like region of the plot (Figure 8C). These results confirm the hints obtained from SEC experiments and support the classification of the W proteins within the PMG-like sub-family of IDPs.
Protein: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The pairiwse distance distribution, P(r), yielded a maximal dimension, Dmax, of ~240 Å for HeV and ~245 Å for NiV W (Supplementary Figure S6C) with a long tail in the P(r) function, indicating that the proteins assume an overall non-compact conformation [69].
The flexible nature of the W proteins was also qualitatively assessed using the Kratky- Debye and the normalized Kratky plots (Figure 10C,D). The presence of a plateau in the Kratky-Debye plot (Figure 10C) and the shape of the normalized Kratky plot (with no clear maximum) (Figure 10D) indicate that the W proteins are intrinsically disordered.
For both proteins, the resulting final Rg (Figure 10E,F) and Dmax (Supplementary Figure S6D) distributions, are unimodal and close to those of the initial pool, indicating that the W proteins exist in solution as randomly distributed ensembles of non-compact and highly flexible conformations.
In conjunction with all the other experimental lines of evidence presented above, SAXS data definitely demonstrate that the W proteins are intrinsically disordered. 
Cross-references: SASBDB:SASDLL9
Protein: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
Annotation: disorder (Structural state)
Evidence: protein thermal shift assay evidence used in manual assertion
Supporting statements:
The experimentally observed profile obtained for both the W proteins does not feature any transition peak, consistent with the lack of a stable 3D structure (Figure 6). These results provide additional support for an overall disordered nature of the W proteins, in line with the in-silico analyses and with the above-described experimental lines of evidence.