LiteFold/DisProt huggingface dataset:
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 441	to 450
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1430	to 1478
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1497	to 1513
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1543	to 1554
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1566	to 1575
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1615	to 1664
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1679	to 1690
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the main chain in ATG2A could be traced except for two long loop regions (residues 304–424 and 1237–1416) that were not visible in the map (Fig. 1a). The N-terminal domain responsible for lipid extraction and ATG_C were also too flexible to directly model.
The Cryo-EM structure deposited in PDB shows this region lacks electron density, indicating it is also disordered. 
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 12	to 16
Annotation: lipid transfer activity (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
The transfer of NBD–PE and/or rhodamine–PE to acceptor liposomes, as well as the transfer of nonfluorescent lipids to donor liposomes, would result in FRET pair dilution and an increase in NBD fluorescence (Fig. 3f). The wild-type ATG2A can transfer lipids between donor and acceptor liposomes, resulting in increased NBD fluorescence. All three mutants showed substantially reduced activity relative to the wild-type protein, which confirms the simulation predictions (Fig. 3g).
Cross-references: PDB:8KBY
EMDB:37087
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1374	to 1404
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Based on the primary sequence analysis of ATG2, we removed the N-terminal 15 residues from this region and used the two fragments of ATG2A (the long fragment (1358–1404) and short fragment (1374–1404), referred to as ATG2Along and ATG2Ashort, respectively) tagged with GB1 for the isothermal titration calorimetry (ITC) assay (Supplementary Fig. 1a, b). As the control, GB1 alone did not bind to WIPI3, but both ATG2Along and ATG2Ashort bound to WIPI3 with a similar affinity (with the Kd of 8.6 ± 0.1 μM and 8.7 ± 0.1 μM, respectively) (Supplementary Fig. 1c), indicating that the N-terminal 15 residues of ATG2Along is not involved in the binding to WIPI3. Thus, ATG2Ashort could be the minimum WIPI-interacting region in ATG2A for binding to WIPI3 and was referred to as the WIR-peptide.
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1378	to 1399
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The complex structure was determined by the molecular replacement method and refined to 2.2 Å (Supplementary Table 1). The WIR-peptide of ATG2A was resolved (from 1378 to 1399) based on its electron density map (Fig. 1a–c). Consistent with the stoichiometry of 1:1 in the ITC assay, a single WIR-peptide binds to WIPI3-Δloop (Fig. 1b and Supplementary Fig. 1d).
From overall structure, the WIR-peptide spans across blades 1–3 and binds to multiple inter-blade sites embedded in the β-propeller (Fig. 1d, e).
Cross-references: PDB:6KLR
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1374	to 1404
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
We made point mutations in each part of the WIR-peptide (V1381Q, I1389Q, V1391Q, Y1395A, and F1396A) to evaluate the essential roles of these residues for binding to WIPI3. As expected, all the mutations severely impaired the binding to WIPI3-Δloop (Fig. 3e and Supplementary Fig. 6). Consistent with mutational studies of WIPI3 (Fig. 3a), mutations in the middle segment and C-terminal tail of the WIR-peptide have more impact on the binding (Fig. 3e), supporting the primary roles of M-site and C-site and the auxiliary function of N-site.
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1381	to 1396
Annotation: protein binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
As expected, mutations in each part of the WIR-motif in ATG2A (V1381Q, T1382Q, I1389Q, Y1395A, and F1396A) decreased the binding to WIPI4 (Fig. 3f), supporting that the WIR-motif is essential for ATG2A to interact with WIPI4.
Protein: DP02142 (UniProt Q2TAZ0)
Region: residues 1381	to 1396
Annotation: positive regulation of autophagy (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
In contrast, transfection of all the WIR-motif mutants (V1381Q, T1382Q, I1389Q, Y1395A, and F1396A) could not rescue the depletion defect (Fig. 4a, b). Although the cellular level of LC3-positive structures was also increased after adding bafilomycin A1, the increments of LC3-positive clusters (with transfection of the ATG2A mutants) were significantly lower than that upon transfection of wild-type ATG2A (Supplementary Fig. 8). Thus, the conserved WIR-motif in ATG2A mediates the binding to WIPI4 and is essential for the ATG2A-mediated autophagic process.
Moreover, the formation of the ATG2A/WIPI4 complex was proposed to be important for the expansion and maturation of autophagosome and depletions of ATG2 proteins in mammalian cells led to the accumulation of immature phagophores21,28.
Protein: DP02143 (UniProt O67086)
Region: residues 90	to 118
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure 4B:  Partially unfolded C terminus of form 2. Arg 90 and Lys 91 form salt bridges with Glu 87 and Asp 95, respectively.
Cross-references: PDB:2GHJ
Protein: DP02143 (UniProt O67086)
Region: residues 1	to 59
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
L20 shows a highly charged α-helical amino-terminal extension (aa 1–59) that contains clusters of conserved basic residues involved in RNA contacts in the ribosome.
Cross-references: PDB:2GHJ
Protein: DP02143 (UniProt O67086)
Region: residues 1	to 59
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Indeed, nuclear magnetic resonance studies have indicated that L20 extension is fully unstructured in the absence of its RNA target (Raibaud et al, 2002).
Protein: DP02144 (UniProt P32337)
Region: residues 80	to 90
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues 80–90 of Kap121p correspond to a loop connecting HEATs 2 and 3, which has no electron density in Kap121p–RanGTP complex. Truncation of this loop was vital to obtain crystals of Kap121p–cargo complexes, Kap121p–Nup53p complex, and unliganded Kap121p.
Cross-references: PDB:3w3y
Protein: DP02144 (UniProt P32337)
Region: residues 80	to 90
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues 80–90 of Kap121p correspond to a loop connecting HEATs 2 and 3
Protein: DP02145 (UniProt P47054)
Region: residues 328	to 424
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The D2 domain contains two long loops: (L1) a long, ~100 amino acid (residues 328–424) loop that seems to adopt a mostly random coil conformation, within which residues 363–416 could not be modeled in the electron density maps and (L2) an ~30 amino acid loop (residues 575–601) that could not be modeled in the electron density maps
Cross-references: PDB:4ifq
Protein: DP02145 (UniProt P47054)
Region: residues 576	to 601
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The D2 domain contains two long loops: (L1) a long, ~100 amino acid (residues 328–424) loop that seems to adopt a mostly random coil conformation, within which residues 363–416 could not be modeled in the electron density maps and (L2) an ~30 amino acid loop (residues 575–601) that could not be modeled in the electron density maps
Cross-references: PDB:4ifq
Protein: DP02145 (UniProt P47054)
Region: residues 799	to 813
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The D3 domain of ScNup192(2–960) has a globular shape composed of 15 helices (from α35 to α49) and includes two disordered loop regions (residues 799–813 between α41 and α42 [L3], and residues 850–856 between α44 and α45 [L4]).
Cross-references: PDB:4ifq
Protein: DP02148 (UniProt Q676U5)
Region: residues 59	to 84
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
All the selected IDRs lack α-helical structure in solution
However, the marginal secondary structure content suggests that all the peptides tested are IDRs.
Protein: DP02148 (UniProt Q676U5)
Region: residues 12	to 31
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The marked chemical shift deviation of CαH resonances of
K30 from the random coil values also supports a folded
conformation of peptide K30 in D8PG micelles.
Cross-references: PDB:5ZYX
Protein: DP02149 (UniProt Q24570)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-3, Table 3-5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues. Formation of a minimal beta-structure requires six residues [38], and seven of the thirteen IDRs (Table 3-5) appear to have between six to eight residues in extended or β-conformation which may be sufficient for forming short stable β-hairpins (Table 3-5). Thus, while none of the selected IDRs had stable helical structure, several may have short β-strands.
Protein: DP02150 (UniProt Q9HD26)
Region: residues 248	to 277
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-3, Table 3-5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues. Formation of a minimal beta-structure requires six residues [38], and seven of the thirteen IDRs (Table 3-5) appear to have between six to eight residues in extended or β-conformation which may be sufficient for forming short stable β-hairpins (Table 3-5). Thus, while none of the selected IDRs had stable helical structure, several may have short β-strands.
Protein: DP02150 (UniProt Q9HD26)
Region: residues 255	to 279
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-3, Table 3-5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues. Formation of a minimal beta-structure requires six residues [38], and seven of the thirteen IDRs (Table 3-5) appear to have between six to eight residues in extended or β-conformation which may be sufficient for forming short stable β-hairpins (Table 3-5). Thus, while none of the selected IDRs had stable helical structure, several may have short β-strands.
Protein: DP02151 (UniProt Q925J9)
Region: residues 637	to 654
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure content estimated by analysis of CD spectra for each of the thirteen IDRs showed that none contained more than two residues in a helical conformation (Figures 1-3, Table 3-5), which is insufficient for the formation of a stable α-helix requiring a minimum of six residues. Formation of a minimal beta-structure requires six residues [38], and seven of the thirteen IDRs (Table 3-5) appear to have between six to eight residues in extended or β-conformation which may be sufficient for forming short stable β-hairpins (Table 3-5). Thus, while none of the selected IDRs had stable helical structure, several may have short β-strands.
Protein: DP02155 (UniProt P49687)
Region: residues 606	to 734
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 in situ yeast NPC shows this region of the NUP145 protein is disordered. 

Cross-references: PDB:7N9F
Protein: DP02156 (UniProt P46673)
Region: residues 1	to 46
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 Nup85-Seh1 from S. cerevisiae bound by nanobodies shows this region lacks electron density, indicating it is disordered. The nanobodies are single-domain (VHH) antibody fragments derived from camelid heavy-chain only antibodies.
Cross-references: PDB:6X08
Protein: DP02156 (UniProt P46673)
Region: residues 432	to 450
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 Nup85-Seh1 from S. cerevisiae bound by nanobodies shows this region lacks electron density, indicating it is disordered. The nanobodies are single-domain (VHH) antibody fragments derived from camelid heavy-chain only antibodies.
Cross-references: PDB:6X08
Protein: DP02157 (UniProt P35729)
Region: residues 30	to 52
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Because the major part of the surface-exposed 1E1A and 5CD loops (residues 30–52 and 306–310) are invisible in the electron density, presumably due to disorder, these 2 regions were omitted from the final model.
Cross-references: PDB:3h7n
Protein: DP02158 (UniProt P36161)
Region: residues 1	to 55
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Secondary structure predictions and limited proteolysis experiments suggest that the ≈55 N-terminal residues also are unstructured in the yeast Nup133 NTD. We refer to this 55-residue fragment (residues 1–55) as the N-terminal extension (NTE). Using circular dichroism spectroscopy, we confirmed a random coil conformation of the Nup133 NTE.
Protein: DP02158 (UniProt P36161)
Region: residues 1	to 55
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
"Further analysis revealed that an N-terminal Nup133 fragment containing only residues 1–15 was sufficient for complex formation with Nup120."
Cross-references: PMID:19706512
Protein: DP02160 (UniProt P61328-2)
Region: residues 148	to 181
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4JQ0
Protein: DP02162 (UniProt P16050)
Region: residues 22	to 162
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism spectra of
LOX-PP showed a single minimum near 200 nm, which is characteristic of an intrinsically disordered protein
(IDP) (Fig. 2a). Te content in secondary structure of LOX-PP was calculated by deconvoluting the spectra with
CONTIN-LL. Te content in α-helix and β-sheet was found to be 3.4% and 20.4% respectively, whereas the turn
content was 11.8%, and the disorder 64.5%.
Protein: DP02163 (UniProt Q02388)
Region: residues 1940	to 1978
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To gain insight into the potential function of the hinge region we investigated a heterologous expressed peptide by CD and NMR spectroscopy. CD spectroscopy implies that the hinge region is intrinsically disordered. Resonance assignment was performed and allowed secondary structure analysis based on the chemical shift values. Seven amino acids in the N-terminal moiety show residual α-helical conformation.
The CD spectrum (Fig. 3 a) of the hinge peptide shows a negative minimum at 200 nm and a negative shoulder at about 220 nm at 5 °C that are characteristic for intrinsically disordered proteins (Kjaergaard et al., 2010).
(b) Monitoring the CD signal at 200 nm indicates that alterations in the CD spectrum are not due to unfolding. Temperature dependency of the CD signal at 220 nm is provided in the supplemental information (supplemental Fig. A1).
It was speculated that the hinge region might represent the trimerization domain of Col7 due to the presence of heptad repeats characteristic for coiled coil structures (McAlinden et al., 2003). However, CD spectroscopy clearly demonstrates that the hinge region does not adopt a coiled coil structure under the employed experimental conditions. Moreover, the CD-spectrum of the hinge region is typical for an intrinsically disordered protein. The negative shoulder at 220 nm can be interpreted as residual α-helical structure. This is in line with data obtained by NMR spectroscopy: (I) there is no signal dispersion observed in an 1H,15N-HSQC spectrum indicating the absence of secondary structure and (II) secondary structure prediction based on chemical shifts identified only seven amino acids (R24, L25, E27, T28, K32, A33, and S34) with dihedral angles corresponding to an α-helical conformation. The presence of residual secondary structure is commonly observed in disordered proteins (Dunker et al., 2002, Tompa, 2002).