LiteFold/DisProt huggingface dataset:
Protein: DP01148 (UniProt A0A068MVV3)
Region: residues 1	to 65
Annotation: protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Because GS and IF7 sizes are very different, it is clear that GS scattering contribution dominates SAXS data. However, the fact that the experimental curve, corresponding to the simultaneous presence of GS and IF7 in solution, was different from the sum of the single scattering contributions of the two isolated proteins, confirms the presence of a well defined assembly arrangement between IF7 and GS. Although the presence of the IF7/GS complex in solution is well-documented [6,9,25], our SAXS results provide a direct estimation of some of its structural features at a low resolution.
Protein: DP01148 (UniProt A0A068MVV3)
Region: residues 1	to 65
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The addition of GS in submicromolar concentrations to IF7 did not change the chemical shifts of the cross-peaks in the HSQC spectrum of IF7 (Fig. S1, Table ST2), although it induced signal broadening as it happened in the cross-peaks of other IDPs when bound to their partners [22,57, and references therein]. In general, we observed an increase in all the relaxation rates of IF7, when compared to those measured in the absence of GS (Fig. 2).
All the NOE values showed the same tendency described in the absence of GS, indicating that IF7 kept its disordered state when it is bound.
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum showed a single minimum at approximately 200 nm (Fig. 2A) that is indicative of random or disordered secondary structure.
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N HSQC spectrum of BECN1(1–150)[4CS]Y (Fig. 2B) displayed very narrow chemical shift dispersion (between 7.7 and 8.7 ppm) on the 1H dimension that is a characteristic feature of intrinsically disordered proteins.
Experimentally observed backbone chemical shifts of BECN1(1–150)[4CS]Y were then used to evaluate its secondary structure with the improved version of Chemical Shift Index software (CSI 2.0)34 which makes use of all 6 backbone chemical shifts (13Cα, 13Cβ, 13C, 15N, 1HN, and 1Hα), along with sequence-derived features. This analysis confirmed that BECN1 is disordered throughout its entire N terminus (1 to 150) except for a potential half-helical turn involving residues A44 and P45 (Fig. 2C).
Cross-references: BMRB:25384
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Previously reported backbone chemical shifts of BecN-150CSY (http://www.bmrb.wisc.edu, Accession code: 25384) [16] were further analysed using the δ2D method [30] and the results are summarized in Figure 2. As expected, BecN-150CSY is predominantly random coil (Fig. 2A) which is consistent with results from Chemical Shift Index analysis using CSI 2.0 [15] as reported previously [16], though a slightly higher propensity of α-helical conformation was observed for residues adjacent to the BH3 domain (Fig. 2B) when compared with the rest of BecN-150CSY.
Using dioxane with a hydrodynamic radius of 2.12 Å as an internal reference (Eq. 2 [29]), Rh values for BecN-150CSY were calculated to range from 29.5 to 31.4 Å across the temperature range studied, with a mean value of 30.54 ± 0.68 Å. This Rh value of BecN-150CSY is in very good agreement with those reported previously for IDPs of approximately the same size, such as α-synuclein (140 amino acid residues, Rh ~ 29 Å [36]) and MSP2 (229 amino acid residues, Rh ~ 34 -39 Å [37]). Similarly, using the relationship between Rh and the number of residues, N, for IDPs, Rh IDP = 2.49 N 0.509 as reported by Marsh and Forman-Kay [38], an expected value of 32.3 Å for BecN-150CSY was obtained which again is in excellent agreement with Rh values derived from the PFG-NMR measurements.
As the temperature coefficients of backbone amide protons over the entire BecN-150CSY were well below -4.5 ppb K -1, this indicates that the backbone amide protons are not involved in any stable hydrogen bonds [40-42] and is in agreement with the characteristics of an intrinsically disordered protein
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
Unlike globular proteins, where amide protons involved in hydrogen bonding will display slow solvent exchange with the solvent (in the order of minutes or slower) and typically have a temperature coefficient more positive than -4.5 ppb/K, [41], no simple correlation between relatively rapid solvent exchange rates (Fig. 5B) and the measured temperature coefficients (Fig. 3C) were observed in the present study. Even in the presence of a 14 amino acids N-terminal purification tag, the residues that undergo the most significant exchange with the solvent water are near the N-terminus of BecN-150CSY. Notably, no significant difference in solvent exchange was observed for residues within the BH3 domain, hence, the degree of surface exposure, compared to the rest of the N-terminal domain.
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
Upon gel-filtration chromatography, the major protein-containing peak eluted at an earlier retention time than expected for a protein of the calculated molecular mass based on the amino acid sequence (Fig. 1B). 
These data demonstrated that the protein exists as a 1.2S monomer (Fig. 1C), hence the behavior on gel-filtration is indicative of the protein being intrinsically disordered rather than oligomeric.
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: analytical ultracentrifugation evidence used in manual assertion
Supporting statements:
The highly elongated shape of the molecule, as determined by its high frictional ratio in the sedimentation velocity experiment (f/f0: 2.2), is also a characteristic of an intrinsically disordered protein.
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 150
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The slightly anomalous migration on SDS-PAGE is likely due to the high positive charge content of the molecule, another characteristic of an intrinsically disordered protein.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
In solution competition assays, the IC50 (2.0 μM) value of BECN1(1–150)[4CS]Y was similar to that of a synthetic peptide whose sequence overlaps with the BECN1(BH3) domain (IC50 2.9 μM) and consistent with previously published binding data on BECN1(BH3) domain peptides.10,12,16 The similarity in the values between the BECN1(BH3) peptide and the entire N-terminal domain suggests the protein produced is fully functional and that regions outside of the BH3 domain are not involved in interactions with BCL2 family members.
BH3 domain of Beclin-1 corresponds to the region 105-130
Protein: DP01149 (UniProt Q14457)
Region: residues 98	to 132
Annotation: disorder to order (Structural transition)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
When BCL2L1ΔC25 was titrated into the BECN1(1–150)[4CS]Y sample, only resonances located within or adjacent to the BH3 domain (residues 98 to 132) were significantly perturbed (Fig. 3A to H) with only a small number of new resonances detected in the BCL2L1ΔC25-bound form (highlighted in cyan circles in Fig. 3A). This indicates the exchange between the free and bound conformations of BECN1(1–150)[4CS]Y is intermediate (in the millisecond range) on the NMR chemical shift timescale.
BH3 domain of Beclin-1 corresponds to the region 105-130
Interestingly, the large majority of resonances of BECN1(1–150)[4CS]Y were completely unaffected (both peak intensity and linewidth) by the binding of its BH3 domain with BCL2L1ΔC25 (except for a small loss in intensity in residues adjacent to Q40, Fig. 3B), indicating that nearly all residues outside of the BH3 domain are tumbling as freely when bound to BCL2L1 as in the unbound form, and do not adopt any secondary or tertiary structure elements that are not present in the free form.
In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor.
More importantly, our NMR analysis showed that upon binding to BCL2L1, the whole of the N-terminal region except the BH3 domain remains unstructured, suggesting that this interaction does not “nucleate” additional structural transitions beyond the formation of the α-helical BH3 domain.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: order (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor.
BH3 domain of Beclin-1 corresponds to the region 105-130
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
When BCL2L1ΔC25 was titrated into the BECN1(1–150)[4CS]Y sample, only resonances located within or adjacent to the BH3 domain (residues 98 to 132) were significantly perturbed (Fig. 3A to H) with only a small number of new resonances detected in the BCL2L1ΔC25-bound form (highlighted in cyan circles in Fig. 3A). This indicates the exchange between the free and bound conformations of BECN1(1–150)[4CS]Y is intermediate (in the millisecond range) on the NMR chemical shift timescale.
BH3 domain of Beclin-1 corresponds to the region 105-130
Interestingly, the large majority of resonances of BECN1(1–150)[4CS]Y were completely unaffected (both peak intensity and linewidth) by the binding of its BH3 domain with BCL2L1ΔC25 (except for a small loss in intensity in residues adjacent to Q40, Fig. 3B), indicating that nearly all residues outside of the BH3 domain are tumbling as freely when bound to BCL2L1 as in the unbound form, and do not adopt any secondary or tertiary structure elements that are not present in the free form.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
As expected for disordered peptides,23, 24 the 1D-1H NMR spectra (Figure 3A) measured for the BH3D lacked peaks upfield of the strong methyl peaks at 0.8 ppm; contained broad peaks at about 8.3 ppm, the region characteristic for amide groups in random-coil conformation; and had little signal dispersion visible downfield of ~8.5 ppm, with the few peaks visible below 8.5 ppm being attributable to Trp sidechains.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
The BECN1 BH3D CD spectra showed a large single negative transition at ~195 nm, indicative of a random coil conformation (Figure 3B); compared to the CD spectra of α-helical polypeptides which are expected to display a positive band at ~192 nm and a large negative split transition at 208 nm and 222 nm; and of β-strand polypeptides which would show a positive band at 195 nm and a negative band at 218 nm.
In contrast to the isolated BH3D, the molar ellipticity at 222 nm indicated that a BECN1 BH3D+HD+CCD construct has a much higher helical content, although not as high as that observed for a HD+CCD construct. This reduction in helical content suggests that the BH3D is disordered even when attached to the helical domains that follow it.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
ITC measurements indicate that the BECN1 BH3D binds to BCL2 with a Kd of 10.4 μM (Table IV). Binding is abolished by Ala substitutions of the single residues L112, L116, or F123, as well as the double G120E+D121A substitution (DS).
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: order (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
This secondary structure content is unchanged upon addition of equimolar or 0.5-fold molar BECN1 BH3D, suggesting that the BH3D folds into a helix upon binding (Table III).
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: disorder to order (Structural transition)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
This secondary structure content is unchanged upon addition of equimolar or 0.5-fold molar BECN1 BH3D, suggesting that the BH3D folds into a helix upon binding (Table III). However, addition of a 10-fold molar excess of the BH3D reduces the helical content of the sample to 76%, consistent with a significant population of BH3D molecules being in a random coil conformation. In contrast to the BH3D, addition of equimolar or 10-fold excess molar DS BH3D peptide dramatically reduces the helical content of the sample to ~67% and ~45% respectively, indicating that there is no change in the secondary structure of the DS BH3D peptide, consistent with lack of binding to BCL2s.
Thus, the combined information from IDR predictions, CD, NMR and co-complex crystal structures indicates that the BECN1 BH3D undergoes a disorder to αhelix transition upon binding.
Protein: DP01149 (UniProt Q14457)
Region: residues 141	to 156
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density corresponding to residues 141–156 is missing, suggesting that similar to the BH3D preceding it (16), this region may be unstructured in certain physiological contexts.
Cross-references: PDB:5EFM
Protein: DP01149 (UniProt Q14457)
Region: residues 104	to 131
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
A 72 residue fragment (residues 104–175) in the N-terminal region of Beclin-1 was found to bind robustly to Bcl-xL in a pull down assay (Figure 1(a)). Deletion of residues 104–131 eliminated interaction between Beclin-1 and Bcl-xL (Figure 1(a)), indicating that this 28 residue fragment of Beclin-1 is required for the protein to interact with Bcl-xL.
We further noted that Trx-Beclin-1 (104-131) binds to GST-Bcl-xL in a similar manner when compared to Trx-Beclin-1 (104-175), suggesting that the 28 residue fragment of Beclin-1 (residues 104–131) is likely to be sufficient for binding to Bcl-xL.
Protein: DP01149 (UniProt Q14457)
Region: residues 104	to 131
Annotation: protein binding (Molecular function)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Mixing a peptide fragment encompassing Beclin-1 (104-131) (Figure 1(d) and (e)), but not its immediate C-terminal fragment (residues 132–175, data not shown), with Bcl-xL induced large chemical shift changes to a subset of resonances in the 1H-15N heteronuclear single quantum coherence (HSQC) spectrum of 15N-labeled Bcl-xL, further supporting that the 28 residue fragment of Beclin-1 (residues 104–131) binds to Bcl-xL specifically. 
Cross-references: PDB:2PON
Protein: DP01149 (UniProt Q14457)
Region: residues 104	to 131
Annotation: protein binding (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
We found that Bcl-xL binds to Beclin-1 (104-131) with a relatively high affinity (Kd ∼1.4 μM) (Figure 1(c)). Longer Beclin-1 fragments with extensions in both the N and C termini of this 28 residue peptide did not increase the binding affinity of Beclin-1 to Bcl-xL (data not shown), further demonstrating that the 28 residue peptide fragment identified here represents the complete Bcl-xL-binding domain of Beclin-1.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Analysis of these NMR spectra showed that binding of the Beclin 1 BH3 domain affects extensive regions of M11, including not only residues of the hydrophobic groove and those that undergo conformational changes, but also residues from other regions of M11 (Fig. 2A).
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Our 2.5 Å crystal structure of the M11-Beclin 1 BH3 domain complex (Fig. 1) shows that the Beclin 1 BH3 domain binds to a hydrophobic surface groove on M11, similar to the binding of BH3 domains of proapoptotic proteins to other antiapoptotic Bcl-2s.
Cross-references: PDB:3DVU
Protein: DP01149 (UniProt Q14457)
Region: residues 1	to 135
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The Beclin 1 (1–135) fragment binds to γHV68 M11 with approximately 40-fold higher affinity than cBcl-2 and 65-fold higher affinity than KSHV Bcl-2 (Table 1).
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The Beclin 1 (1–135) fragment binds to γHV68 M11 with approximately 40-fold higher affinity than cBcl-2 and 65-fold higher affinity than KSHV Bcl-2 (Table 1).
Thus, compared to the Beclin 1 BH3 domain, the 1–135 fragment binds approximately five-fold more strongly to M11, but does not bind significantly better to either cBcl-2 or KSHV Bcl-2.
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: regulation of autophagy (Biological process)
Evidence: green fluorescent protein fusion protein localization evidence used in manual assertion
Supporting statements:
Beclin 1-dependent, starvation-induced autophagy levels are downregulated by cBcl-2 (p < 0.001 for cBcl-2 versus empty vector), and even more potently by KSHV Bcl-2 (p < 0.0003 for KSHV Bcl-2 versus empty vector).
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
We first solved a structure of BCL2 bound to wild-type BECN1 BH3 (PDB code 5VAU, Table 2). This structure has four molecules in the asu, affording four views of the interaction (Figure 3(a)).
Cross-references: PDB:5VAU
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
The wild-type BECN1 BH3 yielded IC50 values consistent with what we and others have reported previously for binding to BCL2L1 [3,4,18–20], while the p-T108 peptide bound slightly, though significantly, tighter (2.0 μM versus 1.2 μM, p < 0.0001) (Table 1, Figure S1(a,b)).
Protein: DP01149 (UniProt Q14457)
Region: residues 96	to 102
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
PIK3C3, BECN1 and ATG14 WT LIR motifs bound to GABARAPL1 in and extended conformation with the two core hydrophobic residues in position 0 and +3 deeply bound to the hydrophobic pockets HP1 and HP2.
The specific interactions observed in WT BECN1 structures were: 1) Hydrophobic contact between L99 (BECN1) in position +2 and the edge of HP2; 2) two hydrogen bonds between the guanidine of R28 (GABARAPL1) and the carbonyls of G101 (BECN1)-L100 (BECN1), as well as a third one between the carbonyl of N95 (BECN1) (or the side chain of S96 for the peptide structure) and the side chain of K48 (GABARAPL1) (Figure 5(a,b)).
BECN1 LIR motif coresponds to the 97-100 region.
Cross-references: PDB:6HOI
PDB:6HOJ
Protein: DP01149 (UniProt Q14457)
Region: residues 76	to 105
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show the region is intrinsically unstructured by itslarge negative ellipticity at 200 nm and moderate ellipticity at 190 nm, typical of IDR
Protein: DP01149 (UniProt Q14457)
Region: residues 50	to 78
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show the region is intrinsically unstructured by itslarge negative ellipticity at 200 nm and moderate ellipticity at 190 nm, typical of IDR
Protein: DP01149 (UniProt Q14457)
Region: residues 105	to 130
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Authors show the region is intrinsically unstructured by itslarge negative ellipticity at 200 nm and moderate ellipticity at 190 nm, typical of IDR
Although none of these IDRs have a helical content sufficient for formation of a stable helix in the absence of TFE, addition of TFE induces a significant disorder-to-helix transition in all three IDRs (Table 4).
Protein: DP01149 (UniProt Q14457)
Region: residues 96	to 101
Annotation: protein binding (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The putative core motif of BECN1 (FTLI amino acids F97-I100) was also mutated (F97A, I100A) and tested for interaction with the recombinant GST-Atg8 homologs. The mutations significantly reduced binding and confirmed a functional LIR motif in BECN1 (Figure 2).
Protein: DP01149 (UniProt Q14457)
Region: residues 97	to 100
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
BECN1 only bound with significant affinity to GABARAP and GABARAPL1.
The region includes the canonical LIR motif "FTLI"
Protein: DP01149 (UniProt Q14457)
Region: residues 97	to 100
Annotation: selective autophagy (Biological process)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
The putative core motif of BECN1 (FTLI amino acids F97-I100) was also mutated (F97A, I100A) and tested for interaction with the recombinant GST-Atg8 homologs. The mutations significantly reduced binding and confirmed a functional LIR motif in BECN1 (Figure 2).
The region includes the canonical LIR motif "FTLI"