LiteFold/DisProt huggingface dataset:
Protein: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
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: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
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. 
Cross-references: SASBDB:SASDLL9
Protein: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
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: DP03667 (UniProt P0C1C7)
Region: residues 1	to 450
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: DP03669 (UniProt Q4LE39)
Region: residues 110	to 151
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The structure determination, CSI analysis (19), and TALOS-N results all show that residues 110 to 151 are in fact in a disordered conformation (Fig. S1, B and C, and Fig. 2A).
Cross-references: PDB:7DM4
Protein: DP03669 (UniProt Q4LE39)
Region: residues 110	to 151
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
Besides chemical shift perturbations, addition of dsDNA1 also enhanced NH signal intensities of C-terminal disordered residues of ARID4B TD151, mainly within the sequence 137-GKKTNRGRRS-146 (RGR motif, intensity ratio >3) and Gly110-Ile136 (3 > intensity ratio >1.5) (Fig. 3, D and E).
Cross-references: PDB:7DM4
Protein: DP03669 (UniProt Q4LE39)
Region: residues 121	to 151
Annotation: DNA binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
ARID4B TD121 has an affinity (KD) of ∼110 μM for dsDNA1 estimated by fitting the NMR titration data (Fig. 4, A and B), about five times weaker than ARID4B TD151, which is consistent with the EMSA result. Similarly, the affinity of ARID4B TD121 for dsDNA2 obtained from titration was 237 μM, about three times weaker than ARID4B TD151 (KD 79 μM) (Fig. 4, C–F). Consistent with this, the affinity of ARID4A TD151 with dsDNA1 was measured as 9.7 μM (KD) (Fig. 4, G and H), about 2 to 3 times stronger than ARID4A TD121 (KD 27 μM) (15) and ARID4B TD151 (KD 22 μM). These results confirm that the C-terminal disordered region can enhance DNA-binding affinity of the Tudor domain.
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
 It is noteworthy that the isolated SNARE region of STX17 is intrinsically disordered based on the CD analysis (Fig. 5A), consistent with the aforementioned NMR results (SI Appendix, Fig. S2).
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The small dispersion of the NMR peaks in the 1H dimension of the 1H-15N HSQC spectrum together with the determined secondary structure of this STX17 Qa-SNARE region based on the 13Cα and 13Cβ chemical shift values of each residue after backbone chemical shift assignments indicated that the isolated STX17 Qa-SNARE motif is basically unstructured (SI Appendix, Fig. S2).
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, titration of the 15N-labeled STX17(142–228) with the unlabeled STX17(1–123) protein showed that a selected set of peaks in the 1H-15N HSQC spectrum of STX17(142–228) underwent significant dose-dependent peak broadening or chemical shift changes (Fig. 1B), indicating that the STX17 Qa-SNARE region can specifically interact with the N-terminal Habc domain of STX17. Further plotting of the peak broadening and amide backbone chemical shift changes as a function of residue number revealed that the significant perturbations are mainly rich in the N-terminal part of the STX17 Qa-SNARE motif (residues 174 to 194) (Fig. 1C), suggesting that this region is the major binding site for interacting with the STX17 Habc domain.
The 1H15N HSQC spectra of STX17 Habc domain saturated with STX17(167-215) and STX17(151-196) are almost identical to that with STX17(142-228), suggesting that STX17(167-196) contains the essential sequences for the binding with STX17 Habc domain.
Protein: DP03670 (UniProt P56962)
Region: residues 94	to 121
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Interestingly, we found that the newly appeared NMR peaks arose from residues 94 to 121, which are located in the predicted extreme C-terminal α-helix of the Habc domain (SI Appendix, Fig. S1A), but were demonstrated to be unstructured in the presence of STX17(142–228) based on our NMR analysis (SI Appendix, Fig. S4C).
Protein: DP03670 (UniProt P56962)
Region: residues 94	to 121
Annotation: order to disorder (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Taken together, all these data clearly demonstrated that the Qa-SNARE motif of STX17 can directly bind to the STX17 Habc domain and alter its conformation by partially unfolding its extreme C-terminal α-helix.
STX17 SNARE region is comprised by the 167-224 residues and the Habc domain by the 1-123 residues.
However, unlike that of Syntaxin1, the binding of the STX17 SNARE motif to its Habc domain can induce a partial unfolding of the extreme C-terminal α-helix of the STX17 Habc domain (Fig. 1D and SI Appendix, Fig. S4C).
Protein: DP03670 (UniProt P56962)
Region: residues 94	to 121
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR-based analyses showed that both GABARAP and LC3A can interact with STX17(142–228) (Fig. 3A and SI Appendix, Fig. S13A), and the major binding sites on STX17 are located within the N-terminal part (residues 170 to 191) of the STX17 Qa-SNARE motif (Fig. 3B and SI Appendix, Fig. S13B).
Protein: DP03670 (UniProt P56962)
Region: residues 171	to 176
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The obtained ITC results showed that the W172Q mutation dramatically reduces and totally abolishes the interaction of STX17(142–228) with GABARAP and LC3A, respectively (Fig. 3 C and D and SI Appendix, Fig. S13 C and D), while the F189Q mutation does not affect the binding of STX17(142–228) to GABARAP and LC3A (Fig. 3 C and E and SI Appendix, Fig. S13 C and E), confirming that only the first putative LIR motif of STX17 is directly involved in the interactions with GABARAP and LC3A (Fig. 3 A and B and SI Appendix, Fig. S13 A and B).
LIR motif corresponds to the 172-175 “WETL” residues.
Protein: DP03670 (UniProt P56962)
Region: residues 167	to 188
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Fortunately, using the purified STX17(167–188)–GABARAP complex, we obtained good crystals that diffracted to 2.0-Å resolution.
Cross-references: PDB:7BV4
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 167
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Lack of electron density in the PDB shows disordered region.
Cross-references: PDB:7BV6
Protein: DP03670 (UniProt P56962)
Region: residues 168	to 228
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To test this hypothesis, we first purified this autophagic SNARE complex, which includes the SNARE motifs of STX17 and VAMP8 together with their short neck regions, and the Qb- and Qc-SNARE motifs of SNAP29, and then used circular dichroism (CD) spectroscopy to examine its secondary structure features and thermal stability.
Protein: DP03670 (UniProt P56962)
Region: residues 168	to 228
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Using analytical gel filtration chromatography-based analyses, we showed that the Qb- and Qc-SNARE motifs of SNAP29 alone are unable to interact with or disturb the GABARAP–STX17 complex (SI Appendix, Fig. S18A); however, in the presence of an additional VAMP8 R-SNARE motif, a stable SNARE complex containing the STX17 Qa-SNARE motif, the VAMP8 R-SNARE motif, as well as the Qb- and Qc-SNARE motifs of SNAP29, was readily formed (SI Appendix, Fig. S18 B and C), indicating that SNAP29 and VAMP8 together can easily compete with GABARAP for binding to STX17 to assemble the STX17–SNAP29–VAMP8 SNARE complex.
Cross-references: PDB:7BV6
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: protein binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Using analytical gel filtration chromatography-based analyses, we showed that the Qb- and Qc-SNARE motifs of SNAP29 alone are unable to interact with or disturb the GABARAP–STX17 complex (SI Appendix, Fig. S18A); however, in the presence of an additional VAMP8 R-SNARE motif, a stable SNARE complex containing the STX17 Qa-SNARE motif, the VAMP8 R-SNARE motif, as well as the Qb- and Qc-SNARE motifs of SNAP29, was readily formed (SI Appendix, Fig. S18 B and C), indicating that SNAP29 and VAMP8 together can easily compete with GABARAP for binding to STX17 to assemble the STX17–SNAP29–VAMP8 SNARE complex.
Cross-references: PDB:7BV6
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: order (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast to that of the isolated SNARE regions of STX17 and VAMP8 as well as the full-length SNAP29, the SNARE complex showed significant characteristic α-helical content, as indicated by its CD spectrum (Fig. 5A).
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast to that of the isolated SNARE regions of STX17 and VAMP8 as well as the full-length SNAP29, the SNARE complex showed significant characteristic α-helical content, as indicated by its CD spectrum (Fig. 5A). It is noteworthy that the isolated SNARE region of STX17 is intrinsically disordered based on the CD analysis (Fig. 5A), consistent with the aforementioned NMR results (SI Appendix, Fig. S2).
Protein: DP03670 (UniProt P56962)
Region: residues 142	to 228
Annotation: self-regulatory activity (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In this model, STX17 alone is in an autoinhibited closed state and, particularly, its Habc region somehow packs with the N-terminal part of its Qa-SNARE motif to stabilize the intrinsically disordered SNARE motif of STX17, thereby preventing its unnecessary degradation or interactions with other proteins on the autophagosome before assembling the STX17–SNAP29–VAMP8 SNARE complex (Fig. 6). However, in the presence of GABARAP/LC3 family proteins, the mammalian ATG8 ortholog can competitively bind to the N-terminal part of the STX17 Qa-SNARE motif that contains an extended LIR motif and abolish the autoinhibited conformation of STX17 (Fig. 6), thereby releasing the N-terminal Habc domain of STX17 and inducing its conformational rearrangement.
Protein: DP03671 (UniProt Q8TDY2)
Region: residues 1543	to 1552
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region lacks electron density, as shown in the PDB, typical of IDR.
Cross-references: PDB:7EA2
Protein: DP03672 (UniProt O95197)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To confirm this, we collected its far-UV CD spectrum at pH 4.0 (Fig. 1A), which has the maximal negative signal located at ∼198 nm, indicating that in solution the hRTN3 N-terminus has no stable secondary structure.
Protein: DP03672 (UniProt O95197)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Moreover, the hRTN3 N-terminus was further 15N isotope-labeled and assessed by 1H–15N NMR HSQC spectroscopy. As clearly seen in Fig. 1B, the hRTN3 N-terminus has a narrowly dispersed HSQC spectrum (∼0.9 ppm for 1H and 20.5 ppm for 15N dimensions). This observation again indicates that hRTN3 C-terminus is also lacking of any tight tertiary packing.
Protein: DP03672 (UniProt O95197)
Region: residues 988	to 1032
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
For the 44-residue hRTN3 C-terminus, we collected its far-UV CD spectra at both pH 4.0 and 6.5 (Fig. 1C), which had the maximal negative signals are located at ∼199 and ∼198 nm, respectively. This indicates that the hRTN3 C-terminus is also highly disordered without any stable secondary structure.
Protein: DP03672 (UniProt O95197)
Region: residues 988	to 1032
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
As seen in Fig. 1D, the hRTN3 C-terminus also has narrowly dispersed HSQC spectra at both pH 4.0 and 6.5 (∼0.65 ppm for 1H and 19.5 ppm for 15N dimensions), suggesting that the hRTN3 C-terminus is also lacking of any tight tertiary packing.
Protein: DP03672 (UniProt O95197)
Region: residues 988	to 1032
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
As seen in Fig. 3A, the binding of hRTN3-C44 to hFADD was associated with the heat absorbance (endothermic), implying that this binding may be mainly entropy-driven [18].
Protein: DP03672 (UniProt O95197)
Region: residues 988	to 1032
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Fig. 3B presents the superimposition of the HSQC spectra of the 15N-labeled hRTN3-C44 in the absence (blue) and presence of hFADD at ratios of 1:1 (green) and 1:2 (red). The obtained result allowed the successful assignment of the perturbed hRTN3-C44 residues upon binding to hFADD.
Protein: DP03674 (UniProt Q9S7A9)
Region: residues 104	to 131
Annotation: disorder (Structural state)
Evidence: magnetic resonance evidence used in manual assertion
Supporting statements:
Flexibility in the C-terminal regions was confirmed by heteronuclear relaxation experiments (data available in Application 1, Image 1, Image 2). 
Cross-references: PDB:1UL4
Protein: DP03675 (UniProt F4K4L7)
Region: residues 182	to 191
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The comparison between the envelope and the NMR structures, with a χ2 = 1.09, confirmed the globular fold of the AtTAF4–RST domain with the addition of a short disordered tail, here originating from the N-terminal end (Fig. 2B).
Cross-references: PDB:7AC1
Protein: DP03675 (UniProt F4K4L7)
Region: residues 182	to 191
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
In addition, the pair distance distribution yielded an average maximal internal distance (Dmax) of 44.4 ± 0.7 Å and described a typical globular protein with a short disordered tail, as evidenced by the Gaussian distribution with an asymmetric end (Fig. S1C).
Cross-references: PDB:7AC1
Protein: DP03676 (UniProt D0NBE6)
Region: residues 370	to 381
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Five N-terminal residues (92–96), the residues in two loops (248–250 and 331–334), and 11 C-terminal residues (371–381), which include the AIM motif, were not included in the final model due to poor electron density in these regions.
Cross-references: PDB:5L7S
Protein: DP03676 (UniProt D0NBE6)
Region: residues 377	to 381
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 Therefore, to visualize the interaction between PexRD54 and ATG8CL, we determined the crystal structure of ATG8CL in complex with a PexRD54 C-terminal pentapeptide. This pentapeptide includes the AIM motif, with residues Asp-377–Trp-378–Glu-379–Ile-380–Val-381.
Cross-references: PDB:5L83
Protein: DP03676 (UniProt D0NBE6)
Region: residues 378	to 381
Annotation: selective autophagy (Biological process)
Evidence: site-directed mutagenesis phenotypic evidence used in manual assertion
Supporting statements:
Site-directed mutagenesis of the PexRD54 C-terminal AIM region, and ATG8CL binding to a PexRD54 AIM-based peptide array, mapped the key residues that define the PexRD54-ATG8CL interface.
First, we used alanine-scanning mutagenesis to substitute Ala at six positions in the PexRD54 AIM region, Pro-373, Asp-377, Trp-378, Glu-379, Ile-380, and Val-381. Each of these proteins was expressed and purified as described for wild type. We then used analytical gel filtration to qualitatively assay whether these variants support complex formation with ATG8CL. As predicted, we did not observe interaction of PexRD54 W378A with ATG8CL (Fig. 7). For each of the other mutations, we still observed an interaction with ATG8CL, including PexRD54 V381A.
FIGURE 7. Analysis of the interaction between PexRD54 variants and ATG8CL by gel filtration. Analytical gel filtration traces were obtained for PexRD54 variants mutated in the AIM region and incubated with ATG8CL (1:1 mixture). 
Full-length RFP-PexRD54 and the AIM motif disrupting variant RFP-PexRD54378-AEIA-381 were used as controls.
The functional LIR motif WEIV in positions 378-381 is inside the disordered fragment region in positions 370-381.
Protein: DP03676 (UniProt D0NBE6)
Region: residues 378	to 381
Annotation: protein binding (Molecular function)
Evidence: site-directed mutagenesis phenotypic evidence used in manual assertion
Supporting statements:
Site-directed mutagenesis of the PexRD54 C-terminal AIM region, and ATG8CL binding to a PexRD54 AIM-based peptide array, mapped the key residues that define the PexRD54-ATG8CL interface.
First, we used alanine-scanning mutagenesis to substitute Ala at six positions in the PexRD54 AIM region, Pro-373, Asp-377, Trp-378, Glu-379, Ile-380, and Val-381. Each of these proteins was expressed and purified as described for wild type. We then used analytical gel filtration to qualitatively assay whether these variants support complex formation with ATG8CL. As predicted, we did not observe interaction of PexRD54 W378A with ATG8CL (Fig. 7). For each of the other mutations, we still observed an interaction with ATG8CL, including PexRD54 V381A.
FIGURE 4. Crystal structure of ATG8CL bound to the PexRD54(377–381)-peptide and specificity of peptide binding. A, schematic representation of ATG8CL/PexRD54(377–381)-peptide complex highlighting key interactions. ATG8CL is shown in magenta schematic representation with the molecular surface that contacts the PexRD54(377–381)-peptide shown in orange. The PexRD54(377–381)-peptide is shown as sticks with yellow carbon atoms. The electron density omit map of the peptide ligand (Fobs − Fcalc map) is shown in blue mesh and contoured at 2 σ. Electrostatic interactions are indicated with black dashed lines. B, results of the peptide array analyzing the effect of single amino acid substitutions (top) at all positions of 10-mer peptide of PexRD54 (Lys-372–Val-381, side). GST-tagged ATG8CL was visualized using an anti-GST-HRP antibody.
FIGURE 7. Analysis of the interaction between PexRD54 variants and ATG8CL by gel filtration. Analytical gel filtration traces were obtained for PexRD54 variants mutated in the AIM region and incubated with ATG8CL (1:1 mixture). 
Full-length RFP-PexRD54 and the AIM motif disrupting variant RFP-PexRD54378-AEIA-381 were used as controls.
The functional LIR motif WEIV in positions 378-381 is inside the disordered fragment region in positions 370-381.