LiteFold/DisProt huggingface dataset:
Protein: DP03709 (UniProt O96018)
Region: residues 1	to 214
Annotation: disorder (Structural state)
Evidence: protein hydrogen-deuterium exchange mass spectrometry evidence used in manual assertion
Supporting statements:
To determine the structural molecular details of the N-terminal regions of Mint3, hydrogen/deuterium exchange–mass spectrometry (HDX-MS) and nuclear magnetic resonance (NMR) spectroscopy were conducted. In the HDX-MS analysis, the exchange events are mediated by the conformational fluctuation of the protein. The exchange rate of amide hydrogen is influenced by the formation of a hydrogen bond, pH, and to a minor degree the temperature (11, 12). In this experiment, the deuteration processes were performed under the condition that the pH and the temperature are well controlled, so that we can focus on the influence of the formation of a hydrogen bond. Therefore, the amide hydrogen of an extended/flexible region will be replaced by solvent deuterium at a higher rate, as compared with that of a folded/rigid region. In fact, the exchange rates of the whole Mint3NT were observed as an immediate saturation in the deuteration level, suggesting an intrinsically disordered state in solution (Figs. 1C and S2A, Table S1A).
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 422	to 469
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered
Cross-references: PDB:7BL1
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 873	to 887
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered
Human complex II-BATS bound to membrane-attached Rab5a-GTP
Cross-references: PDB:7BL1
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 246	to 260
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered
Human complex II-BATS bound to membrane-attached Rab5a-GTP
Cross-references: PDB:7BL1
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 418	to 470
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered
The crystal structure of Human VPS34 in complex with PIK-III
Cross-references: PDB:4PH4
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 872	to 887
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered
The crystal structure of Human VPS34 in complex with PIK-III
Cross-references: PDB:4PH4
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 418	to 434
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered.
CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.
Cross-references: PDB:4OYS
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 452	to 469
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density indicating it is disordered.
CRYSTAL STRUCTURE OF VPS34 IN COMPLEX WITH SAR405.
Cross-references: PDB:4OYS
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 250	to 253
Annotation: selective autophagy (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
For PIK3C3, point mutations of both the aromatic residue and the conserved hydrophobic position (F250A, V253A) of the core LIR-F250 motif (FELV, amino acids 250–253) appeared to significantly reduce binding to the Atg8 homologs.
Region corresponding to the LIR motif "FELV" at position 250-253
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 250	to 253
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Here, the different Atg8 homologs were expressed as GST fusions in E. coli and then tested for interaction with in vitro translated PIK3C3, BECN1 and ATG14, respectively. All the members of PtdIns3K-C1, except PIK3R4, were able to interact with the Atg8 homologs (Figure 2). PIK3C3 and ATG14 showed significant interaction with LC3C and GABARAPL2, but the strongest interaction was seen with GABARAP and GABARAPL1. BECN1 only bound with significant affinity to GABARAP and GABARAPL1. Taken together, PIK3C3, BECN1 and ATG14 all interacted with the Atg8 homologs and appear to have a preference for binding to the GABARAP and GABARAPL1. For PIK3C3, point mutations of both the aromatic residue and the conserved hydrophobic position (F250A, V253A) of the core LIR-F250 motif (FELV, amino acids 250–253) appeared to significantly reduce binding to the Atg8 homologs. In contrast, mutating the core LIR-F198 motif (FREI, amino acids 198–201) in a similar manner (F198A, V201A) did not affect binding of PIK3C3 (Figure 2). This indicates that LIR-F250 of PIK3C3 is the functional LIR motif.
Region corresponding to the LIR motif "FELV" at position 250-253
Protein: DP03710 (UniProt Q8NEB9)
Region: residues 250	to 253
Annotation: selective autophagy (Biological process)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
Here, the different Atg8 homologs were expressed as GST fusions in E. coli and then tested for interaction with in vitro translated PIK3C3, BECN1 and ATG14, respectively. All the members of PtdIns3K-C1, except PIK3R4, were able to interact with the Atg8 homologs (Figure 2). PIK3C3 and ATG14 showed significant interaction with LC3C and GABARAPL2, but the strongest interaction was seen with GABARAP and GABARAPL1. BECN1 only bound with significant affinity to GABARAP and GABARAPL1. Taken together, PIK3C3, BECN1 and ATG14 all interacted with the Atg8 homologs and appear to have a preference for binding to the GABARAP and GABARAPL1. For PIK3C3, point mutations of both the aromatic residue and the conserved hydrophobic position (F250A, V253A) of the core LIR-F250 motif (FELV, amino acids 250–253) appeared to significantly reduce binding to the Atg8 homologs. In contrast, mutating the core LIR-F198 motif (FREI, amino acids 198–201) in a similar manner (F198A, V201A) did not affect binding of PIK3C3 (Figure 2). This indicates that LIR-F250 of PIK3C3 is the functional LIR motif.
Region corresponding to the LIR motif "FELV" at position 250-253
Protein: DP03711 (UniProt Q9BXW4)
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:
The N-terminal α1 helix of LC3C is disordered in our structure; it is possible that this helix is stabilized by acidic residues upstream of canonical LIRs (Noda et al., 2010).
Cross-references: PDB:3VVW
Protein: DP03712 (UniProt Q99623)
Region: residues 246	to 265
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Tha lack of electron density in this region, as shown in the PDB, indicates disorder.
Cross-references: PDB:6IQE
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 53
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N heteronuclear single-quantum coherence (HSQC) spectrum of Tollip TBD was characteristic of an unstructured protein as indicated by the narrow dispersion in the 1HN dimension (Figure 1B).
Cross-references: BMRB:26573
PDB:2N31
BMRB:25632
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 53
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Likewise, the far-UV circular dichroism (CD) spectrum of Tollip TBD displayed a minimum at 200 nm, a feature of unstructured protein spectra (Figure 1B, inset).
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 53
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Titration of the unlabeled Tom1 GAT domain into the 15N-labeled Tollip TBD resulted in dramatic improvement in resonance dispersion (Figure 1C). Resonance perturbations clustered in the first half of Tollip TBD including two N-terminal β strands. The largest chemical-shift perturbations were observed in residues Arg9, Val12, Ile14, Asp20, and Arg23 (Figure 1D).
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 23	to 53
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We therefore measured the internal backbone motions of Tom1 GAT-bound Tollip TBD by analysis of the 1H-15N heteronuclear NOEs and the 15N relaxation times. The 1H-15N NOE profile showed that the first 22 residues of Tollip TBD were highly ordered, whereas the C-terminal half of the protein was disordered (Figure S2A).
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 22
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We therefore measured the internal backbone motions of Tom1 GAT-bound Tollip TBD by analysis of the 1H-15N heteronuclear NOEs and the 15N relaxation times. The 1H-15N NOE profile showed that the first 22 residues of Tollip TBD were highly ordered, whereas the C-terminal half of the protein was disordered (Figure S2A).
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 22
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Together, these data suggest that the conserved N-terminal Tollip TBD becomes ordered upon Tom1 GAT binding, whereas its C-terminal region remains relatively disordered.
Tollip TBD Is Intrinsically Disordered and Partially Folds upon Binding to the Tom1 GAT Domain.
Protein: DP03713 (UniProt Q9H0E2)
Region: residues 1	to 53
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Tollip TBD bound immobilized Tom1 GAT with high association and low dissociation rates, and with an estimated dissociation constant (KD) of 0.67 nM (Table 2 and Figure S4A).
Alanine mutations in Tollip TBD Arg9/Val12 and Asp20/Arg23 reduced Tom1 GAT binding (Table 2 and Figures S4K–S4L). Notably, mutation in Phe21, a conserved residue in Tollip (Figure S1A) that forms several intermolecular NOEs, and its NH backbone resonance is shifted when bound to the Tom1 GAT domain, reducing binding affinity by ∼20,000-fold (Table 2 and Figure S4M). Consequently, the affinity of Tom1 GAT N230A for Tollip TBD F21A showed ∼60,000-fold reduction in the equilibrium constant Kb (data not shown) leading to ∼95,000-fold reduction in binding (Table 2 and Figure S4N), suggesting that these residues reduce the affinity in the initial binding event, and consequently are critical for Tom1-Tollip complex formation.
Protein: DP03714 (UniProt Q12142)
Region: residues 1	to 285
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Using isotopically labeled samples and 1H-15N HSQC NMR, we concluded that, as predicted, the Atg9 NTD (residues 1–285) is largely disordered in solution (Fig. 1C).
Cross-references: BMRB:51011
Protein: DP03714 (UniProt Q12142)
Region: residues 158	to 171
Annotation: protein binding (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
As expected, we observed a robust recruitment of Atg9-NTD(1–255) to the beads coated with EGFP-Atg11 (Fig. 3, A and B). Mutation of the first PLF motif (M1) severely reduced the interaction, and mutation of the second PLF motif (M2) reduced the recruitment of the Atg9-NTD to the EGFP-Atg11-coated beads (Fig. 3, A and B) to a similar extent. Upon mutation of both motifs (M1+M2), the interaction between the Atg9-NTD and Atg11 became undetectable (Fig. 3, A and B).
M1 motiff is comprised of the 158-171 region.
Protein: DP03714 (UniProt Q12142)
Region: residues 158	to 171
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Titration of the wild-type Atg9-NTD(1–255) into full-length Atg11 yielded a robust signal, fitting of which resulted in a KD of around 1 μM and a stoichiometry of 1 (KD = 1,086 ± 0,006 μM, n = 0,931 ± 0,004, Fig. S4). The affinity of the Atg9-NTD(1–255) M1 and M2 mutants for Atg11 was too low to be measured accurately by ITC.
M1 motiff is comprised of the 158-171 region.
Protein: DP03714 (UniProt Q12142)
Region: residues 183	to 196
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Titration of the wild-type Atg9-NTD(1–255) into full-length Atg11 yielded a robust signal, fitting of which resulted in a KD of around 1 μM and a stoichiometry of 1 (KD = 1,086 ± 0,006 μM, n = 0,931 ± 0,004, Fig. S4). The affinity of the Atg9-NTD(1–255) M1 and M2 mutants for Atg11 was too low to be measured accurately by ITC.
M2 motiff is comprised of the 183-196 region.
Protein: DP03714 (UniProt Q12142)
Region: residues 183	to 196
Annotation: protein binding (Molecular function)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
As expected, we observed a robust recruitment of Atg9-NTD(1–255) to the beads coated with EGFP-Atg11 (Fig. 3, A and B). Mutation of the first PLF motif (M1) severely reduced the interaction, and mutation of the second PLF motif (M2) reduced the recruitment of the Atg9-NTD to the EGFP-Atg11-coated beads (Fig. 3, A and B) to a similar extent. Upon mutation of both motifs (M1+M2), the interaction between the Atg9-NTD and Atg11 became undetectable (Fig. 3, A and B).
M2 motiff is comprised of the 183-196 region.
Protein: DP03714 (UniProt Q12142)
Region: residues 183	to 196
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This titration in combination with the assignment allowed us to identify the putative binding site for Atg11 in the Atg9 NTD, which consists of two short stretches (Fig. 2A), both being centered on a PLF motif (Fig. 2B).
Protein: DP03714 (UniProt Q12142)
Region: residues 158	to 171
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This titration in combination with the assignment allowed us to identify the putative binding site for Atg11 in the Atg9 NTD, which consists of two short stretches (Fig. 2A), both being centered on a PLF motif (Fig. 2B).
Protein: DP03715 (UniProt Q02948)
Region: residues 1	to 156
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Interestingly, Vps30 and Vps38 show similar architectures except for their N-terminal domains, where Vps38 has a C2 domain, while Vps30 is mostly unstructured (fig. S3, A and B).
Cross-references: PDB:5DFZ
Protein: DP03715 (UniProt Q02948)
Region: residues 423	to 432
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS30.
Cross-references: PDB:5DFZ
Protein: DP03715 (UniProt Q02948)
Region: residues 463	to 488
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS30.
Cross-references: PDB:5DFZ
Protein: DP03715 (UniProt Q02948)
Region: residues 541	to 557
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS30.
Cross-references: PDB:5DFZ
Protein: DP03716 (UniProt P22219)
Region: residues 170	to 193
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS15.
Cross-references: PDB:5DFZ
Protein: DP03716 (UniProt P22219)
Region: residues 378	to 401
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS15.
Cross-references: PDB:5DFZ
Protein: DP03716 (UniProt P22219)
Region: residues 808	to 833
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS15.
Cross-references: PDB:5DFZ
Protein: DP03716 (UniProt P22219)
Region: residues 887	to 985
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the Vps15 linker between the solenoid and WD40 is disordered (residues 889-985), except for an extended section (residues 986-1050) threading along the surface of Vps34-C2.
Cross-references: PDB:5DFZ
Protein: DP03716 (UniProt P22219)
Region: residues 887	to 985
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Most of the Vps15 linker between the solenoid and WD40 is disordered (residues 889-985), except for an extended section (residues 986-1050) threading along the surface of Vps34-C2.
Cross-references: PDB:5DFZ
Protein: DP03717 (UniProt P22543)
Region: residues 226	to 273
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here, most of the C2/HELCAT linker appeared disordered, however a conserved Linker Helix (Fig. 3C) nestles in a crook between the Vps15 and Vps34, where it could provide a pivot for Vps34-HELCAT motions.
Cross-references: PDB:5DFZ
Protein: DP03717 (UniProt P22543)
Region: residues 226	to 273
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here, most of the C2/HELCAT linker appeared disordered, however a conserved Linker Helix (Fig. 3C) nestles in a crook between the Vps15 and Vps34, where it could provide a pivot for Vps34-HELCAT motions.
Cross-references: PDB:5DFZ
Protein: DP03717 (UniProt P22543)
Region: residues 438	to 477
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS34.
Cross-references: PDB:5DFZ
Protein: DP03718 (UniProt Q05919)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS38.
Cross-references: PDB:5DFZ
Protein: DP03718 (UniProt Q05919)
Region: residues 91	to 110
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS38.
Cross-references: PDB:5DFZ
Protein: DP03718 (UniProt Q05919)
Region: residues 152	to 183
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS38.
Cross-references: PDB:5DFZ
Protein: DP03718 (UniProt Q05919)
Region: residues 322	to 344
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing electron density region of VPS38.
Cross-references: PDB:5DFZ
Protein: DP03718 (UniProt Q05919)
Region: residues 152	to 183
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linker connecting the C2 and CC1 domains of VPS38.
Cross-references: PDB:5DFZ
Protein: DP03719 (UniProt O15392)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, as shown in the PDB, indicating it's disordered.
Cross-references: PDB:4A0N
Protein: DP03719 (UniProt O15392)
Region: residues 1	to 99
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Truncated forms of survivin with only the BIR domain (residues 1−99) have been reported not to interact with Smac/Diablo ( 8) or to localize to the mitotic spindle ( 17). To understand the role of the C-terminal helix for the function of survivin, we cloned and expressed the (residues 1−99) BIR domain only construct. [15N,1H]HSQC spectra for the (residues 1−99) construct did not have the same well- resolved resonances found for full length survivin or our survivin(1−120) construct (data not shown). The lack of well-resolved resonances is characteristic of unfolded or aggregated proteins. This result suggests that the (1−99) construct of survivin is not properly folded. This conclusion is consistent with the structure of the survivin dimer. In the structure, residues 99−110 are involved in making contacts across the dimer interface. These contacts are likely to be important for dimer formation and thus also for protein stability. Removing these key residues is likely to interfere with proper folding of the protein.
Cross-references: BMRB:6342
Protein: DP03721 (UniProt Q9W1M7)
Region: residues 422	to 531
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 indicates it's disordered.
Cross-references: PDB:2X6H
Protein: DP03721 (UniProt Q9W1M7)
Region: residues 423	to 531
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 indicates it's disordered.
Cross-references: PDB:2X6F
Protein: DP03722 (UniProt P01089)
Region: residues 36	to 45
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The first 14 residues, highly disordered, are not represented.
Cross-references: PDB:1PSY