LiteFold/DisProt huggingface dataset:
Protein: DP02033 (UniProt P32504)
Region: residues 1	to 956
Annotation: DNA binding (Molecular function)
Evidence: gel electrophoresis evidence used in manual assertion
Supporting statements:
Both the full-length protein and this fragment were found to be competent for DNA binding against a random (non-centromeric) DNA sequence (Fig. 1b).
Cross-references: PDB:4ACO
Protein: DP02034 (UniProt P62805)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The tail region of hH4 (S1–D24) is not observable in all dipolar‐based experiments due to significant scaling down of the relevant dipolar couplings caused by high flexibility.
However, the N-terminal tail in the array retains structural flexibility as the cross-peaks corresponding to the residues 1–25 are absent in the cross-polarization-based spectra.
Cross-references: BMRB:27457
Protein: DP02035 (UniProt A6QHR2)
Region: residues 323	to 420
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal α/β domain (0–220) and the α-helical domain (248–323) are connected via a linker peptide (221–247),while the C-terminal domain (324–421) is disordered in the crystal (Fig. 2B).
Cross-references: PDB:1JII
Protein: DP02042 (UniProt Q98325)
Region: residues 192	to 241
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of full-length MC159 was first solved at 3.8Å resolution by single-wavelength anomalous diffraction and fourfold non-crystallographic symmetry averaging (Figure 2A). It revealed that more than fifty residues at the C-terminal tail of MC159 were disordered in the crystal.
The structure revealed that a large segment of the C-terminal tail (residues 188–241) is disordered in the crystal. This C-terminal tail is not important for the function of MC159 (Garvey et al., 2002a).
The missing electron density region starts at residue Pro192.
Cross-references: PDB:2BBZ
Protein: DP02042 (UniProt Q98325)
Region: residues 214	to 218
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
To address the relevance of the TRAF consensus-binding motif for the observed interactions, we generated MC159 expression constructs that were either doubly mutated in the first two identical TRAF-binding motifs (MC159 DM) or C-terminally deleted to remove all three potential binding sites (MC159 Δ) (Figure 2a). Co-immunoprecipitation experiments using these MC159 FLIP mutants revealed that the first two TRAF-binding motifs were specifically required for TRAF3 binding, while binding of TRAF1 and TRAF2 did not appear to be affected by the mutation or deletion of these TRAF-binding sites under conditions of overexpression (Figure 2c).
Region corresponding to the first PVQES TRAF-binding motif.
Protein: DP02042 (UniProt Q98325)
Region: residues 228	to 232
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
To address the relevance of the TRAF consensus-binding motif for the observed interactions, we generated MC159 expression constructs that were either doubly mutated in the first two identical TRAF-binding motifs (MC159 DM) or C-terminally deleted to remove all three potential binding sites (MC159 Δ) (Figure 2a). Co-immunoprecipitation experiments using these MC159 FLIP mutants revealed that the first two TRAF-binding motifs were specifically required for TRAF3 binding, while binding of TRAF1 and TRAF2 did not appear to be affected by the mutation or deletion of these TRAF-binding sites under conditions of overexpression (Figure 2c).
Region corresponding to the second PVQES TRAF-binding motif.
Protein: DP02042 (UniProt Q98325)
Region: residues 211	to 241
Annotation: protein binding (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
The double mutant (DM) and the C-terminally deleted form of MC159 FLIP (Δ) failed to bind to TRAF3, as was previously observed under conditions of overexpression in 293T cells (Figure 2c). TRAF2 still bound to both mutants, although at reduced levels, possibly because TRAF3 contributed to optimal recruitment and/or stabilization of endogenous TRAF2 in the complex.
Protein: DP02042 (UniProt Q98325)
Region: residues 228	to 232
Annotation: negative regulation of apoptotic signaling pathway (Biological process)
Evidence: flow cytometry evidence used in manual assertion
Supporting statements:
The percentage of cells that had internalized the receptor correlated well with the percentage of annexin V-positive, apoptotic cells in the same experiments, suggesting that the TRAF3-binding-dependent capacity of MC159 FLIP to inhibit receptor internalization accounted for its antiapoptotic effect (Figure 5c). Together, these data suggest that the intact TRAF3-binding site of MC159 FLIP is required to fully prevent ligand-induced Fas internalization and apoptosis.
Protein: DP02042 (UniProt Q98325)
Region: residues 214	to 218
Annotation: negative regulation of apoptotic signaling pathway (Biological process)
Evidence: flow cytometry evidence used in manual assertion
Supporting statements:
The percentage of cells that had internalized the receptor correlated well with the percentage of annexin V-positive, apoptotic cells in the same experiments, suggesting that the TRAF3-binding-dependent capacity of MC159 FLIP to inhibit receptor internalization accounted for its antiapoptotic effect (Figure 5c). Together, these data suggest that the intact TRAF3-binding site of MC159 FLIP is required to fully prevent ligand-induced Fas internalization and apoptosis.
Protein: DP02049 (UniProt O74774)
Region: residues 1	to 155
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
three regions (residues 1–155, 204–259 and 274–282) in Hbs1 are not visible in the electron density map and are assumed to be disordered.
Cross-references: PDB:3MCA
Protein: DP02049 (UniProt O74774)
Region: residues 204	to 259
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
three regions (residues 1–155, 204–259 and 274–282) in Hbs1 are not visible in the electron density map and are assumed to be disordered.
Cross-references: PDB:3MCA
Protein: DP02050 (UniProt P41814)
Region: residues 61	to 78
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
TRM6 contains 478 amino acid residues, comprising an N-terminal β-barrel domain (residues 1–196) and a C-terminal Rossmann fold domain (residues 197–451). Due to the flexibility, residues 61–78, residues 88–188, residues 322–325 and residues 453–478 are not observed.
Cross-references: PDB:5EQJ
Protein: DP02050 (UniProt P41814)
Region: residues 88	to 188
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
TRM6 contains 478 amino acid residues, comprising an N-terminal β-barrel domain (residues 1–196) and a C-terminal Rossmann fold domain (residues 197–451). Due to the flexibility, residues 61–78, residues 88–188, residues 322–325 and residues 453–478 are not observed.
Cross-references: PDB:5EQJ
Protein: DP02050 (UniProt P41814)
Region: residues 453	to 478
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
TRM6 contains 478 amino acid residues, comprising an N-terminal β-barrel domain (residues 1–196) and a C-terminal Rossmann fold domain (residues 197–451). Due to the flexibility, residues 61–78, residues 88–188, residues 322–325 and residues 453–478 are not observed.
Cross-references: PDB:5EQJ
Protein: DP02051 (UniProt P14335)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Crystals of the full-length C protein were unstable and disordered and did not diffract X-rays to high resolution. Assuming that the crystal disorder was caused by flexible regions in the protein, we treated the full-length protein with trypsin, resulting in a stable fragment starting at Val23 and ending at Arg98 (Figure 1).
 The N-terminal region corresponds to the disordered region (residues 1–22) that was cleaved off by the trypsin treatment, and the C-terminal region corresponds to helix α4, which forms an 11 Å wide tunnel in the tetramer (Figure 3B).
Protein: DP02051 (UniProt P14335)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Crystals of the full-length C protein were unstable and disordered and did not diffract X-rays to high resolution. Assuming that the crystal disorder was caused by flexible regions in the protein, we treated the full-length protein with trypsin, resulting in a stable fragment starting at Val23 and ending at Arg98 (Figure 1).
Protein: DP02055 (UniProt P33322)
Region: residues 351	to 394
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The Cbf5 CTE was not observed in crystal, likely due to protein degradation and intrinsic disorder
Cross-references: PDB:3U28
Protein: DP02061 (UniProt P70447)
Region: residues 49	to 75
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Assignment of the backbone atom resonances of mNgn2 was performed based on 3D experiments on the 15N, 13C doubly-labelled protein (Additional file 4: Table S1, Additional file 5: 3D NMR dataset). This assignment does not cover the full-length protein: the detected domains correspond to residues 1 to 31 and 49 to 75, containing two SP sites and one TP site.
Protein: DP02061 (UniProt P70447)
Region: residues 1	to 31
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Assignment of the backbone atom resonances of mNgn2 was performed based on 3D experiments on the 15N, 13C doubly-labelled protein (Additional file 4: Table S1, Additional file 5: 3D NMR dataset). This assignment does not cover the full-length protein: the detected domains correspond to residues 1 to 31 and 49 to 75, containing two SP sites and one TP site.
Protein: DP02065 (UniProt Q9Y7M4)
Region: residues 56	to 69
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of SpLsm3 was solved by single-wavelength anomalous dispersion (SAD) phasing method using a SeMet-substituted crystal. The final model has been refined to an R factor of 24.3% and Rfree of 27.7% with good stereochemical geometry. Residues 1–8 in the N-terminal and residues 56–69 in the loop region are disordered in the electron density map.
Cross-references: PDB:4EMG
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
AtLEA4-5 was predicted to be disordered based on previous amino acid sequence analysis, while CD spectra showed a typical spectrum for a disorder protein, as indicated by the presence of minimum at ∼200 nm (Fig. S1), in agreement with previous reports (Cuevas-Velazquez et al., 2016).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: copper ion binding (Molecular function)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
These results indicate that AtLEA4-5 coordinates Cu(II) through at least one nitrogen of a histidine imidazole and backbone deprotonated amides.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To determine the secondary structure of AtLEA4-2 and AtLEA4-5 in solution, the purified proteins were analyzed by far UV CD. The results obtained corroborated that both proteins are mostly disordered in solution over a wide range of temperatures (Fig. 2, A and B) and pH (data not shown), with the characteristic negative band for random coil structures around 198 nm.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: zinc ion binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
For Zn(II), Cu(II), and Ni(II) columns, the protein was eluted only when EDTA was added, showing that the protein is able to bind these metal ions (Fig. S2).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: nickel cation binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
For Zn(II), Cu(II), and Ni(II) columns, the protein was eluted only when EDTA was added, showing that the protein is able to bind these metal ions (Fig. S2).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: copper ion binding (Molecular function)
Evidence: affinity chromatography evidence used in manual assertion
Supporting statements:
For Zn(II), Cu(II), and Ni(II) columns, the protein was eluted only when EDTA was added, showing that the protein is able to bind these metal ions (Fig. S2).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: copper ion binding (Molecular function)
Evidence: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
We estimated the binding parameters by plotting average EPR signals changes as function of Cu(II) concentrations. The data was fitted with to a hyperbolic equation and provided an apparent metal binding dissociation constant in the micromolar range (∼300 μM) (Fig. S4).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: protein homooligomerization (Biological process)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
From this we could conclude that under these conditions AtLEA4-5 consist of different states, that include monomer, probably tetramers, and higher order oligomers.
DLS measurements of AtLEA4-5 in the presence of different Cu(II) concentration yielded a decrease in the translational diffusion coefficient consistent with a size increase due to oligomerization induced by metal binding (Fig. 5).
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: copper ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
As shown in Fig. 6, the addition of Ni(II) produced a simple exothermic thermogram, which was best fitted to a single binding site model with a 1:1 stoichiometry; whereas the addition of Cu(II) and Zn(II) exhibited a complex behavior involving both exothermic and endothermic processes.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: zinc ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
As shown in Fig. 6, the addition of Ni(II) produced a simple exothermic thermogram, which was best fitted to a single binding site model with a 1:1 stoichiometry; whereas the addition of Cu(II) and Zn(II) exhibited a complex behavior involving both exothermic and endothermic processes.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 158
Annotation: nickel cation binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
As shown in Fig. 6, the addition of Ni(II) produced a simple exothermic thermogram, which was best fitted to a single binding site model with a 1:1 stoichiometry; whereas the addition of Cu(II) and Zn(II) exhibited a complex behavior involving both exothermic and endothermic processes.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 77
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Together, these data indicate that AtLEA4-2 and AtLEA4-5 can acquire secondary structure under low water availability or macromolecular crowding in vitro, possibly reflecting what occurs in plant cells under water deficit.
Likewise, treatments with glycerol and PEG led to the same behavior in this protein (Fig. 4, C and D), reaching up to 55 and 42% α-helix at the highest glycerol and PEG concentrations, respectively (Table 2).
This finding was further supported by the results obtained from the addition of glycerol or PEG to AtLEA4-578–158 solutions, which showed no effect on its structure (Fig. 4, G and H), given that the negative band at [θ]222 did not show any change and that only a slight increase in the [θ]198 signal was detected.
Together, these data demonstrate that the AtLEA4-5 N-terminal region (AtLEA4-51–77) is necessary and sufficient to drive α-helix conformations in this protein under low water availability or macromolecular crowding conditions.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 77
Annotation: protein stabilization (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
 For this purpose, LDH in the presence or absence of AtLEA4-5, AtLEA4-2, AtLEA4-51–77, or AtLEA4-578–158 was subjected to in vitro freeze-thaw cycles and partial dehydration treatments.
Interestingly, a comparable protection was produced by AtLEA4-51–77, contrasting with the negligible protective levels showed by the AtLEA4-5 C-terminal region (AtLEA4-578–158), whose values were rather close to those shown by lysozyme, an unrelated globular protein (Fig. 5, A and B).
Because the hydrophilicity index and length are similar between the N-terminal and C-terminal regions, these data are consistent with the hypothesis that the protective activity of these proteins is rather dependent on the conserved motifs present in the N-terminal region and/or on its ability to fold into α-helical conformations.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 77
Annotation: cold acclimation (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
 For this purpose, LDH in the presence or absence of AtLEA4-5, AtLEA4-2, AtLEA4-51–77, or AtLEA4-578–158 was subjected to in vitro freeze-thaw cycles and partial dehydration treatments.
Interestingly, a comparable protection was produced by AtLEA4-51–77, contrasting with the negligible protective levels showed by the AtLEA4-5 C-terminal region (AtLEA4-578–158), whose values were rather close to those shown by lysozyme, an unrelated globular protein (Fig. 5, A and B).
Because the hydrophilicity index and length are similar between the N-terminal and C-terminal regions, these data are consistent with the hypothesis that the protective activity of these proteins is rather dependent on the conserved motifs present in the N-terminal region and/or on its ability to fold into α-helical conformations.
Protein: DP02066 (UniProt Q9FG31)
Region: residues 1	to 77
Annotation: response to desiccation (Biological process)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
AtLEA4-2, the smallest protein of this group, mostly consisting of the N-terminal region (Fig. 1A), showed a similar protective effect on LDH activity as AtLEA4-5 after partial dehydration (Fig. 5A).
Protein: DP02067 (UniProt O74499)
Region: residues 1	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions are disordered, namely residues 1–5 and 78–80 in Sp-Lsm5, residues 74–75 in SpLsm6, and residues 1–31, 69–77 and 101–113 in SpLsm7.
Cross-references: PDB:4EMK
Protein: DP02067 (UniProt O74499)
Region: residues 101	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several regions are disordered, namely residues 1–5 and 78–80 in Sp-Lsm5, residues 74–75 in SpLsm6, and residues 1–31, 69–77 and 101–113 in SpLsm7.
Cross-references: PDB:4EMK
Protein: DP02068 (UniProt O14352)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of SpLsm4N was also determined by the SAD method using the data obtained from a SeMet derivative crystal. The structure has been refined at a resolution of 2.2 Å to an R factor of 23.7% and Rfree of 25.2% with good geometry. The final model covers residues 12–71 of every molecule in the AU. Residues 1–11 and 72–91 are not visible in the electron density map and assumed to be disordered
Cross-references: PDB:4EMH
Protein: DP02068 (UniProt O14352)
Region: residues 72	to 91
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of SpLsm4N was also determined by the SAD method using the data obtained from a SeMet derivative crystal. The structure has been refined at a resolution of 2.2 Å to an R factor of 23.7% and Rfree of 25.2% with good geometry. The final model covers residues 12–71 of every molecule in the AU. Residues 1–11 and 72–91 are not visible in the electron density map and assumed to be disordered
Cross-references: PDB:4EMH
Protein: DP02069 (UniProt P38919)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The human EJC core complex was reconstituted combining full-length MAGO bound to the RRM domain of Y14, full-length eIF4AIII bound to the SELOR domain of BTZ,  a U15 RNA, AMPPNP, and magnesium ions. In the final model  eIF4AIII residues 22–411 was observed, other portions of the protein are not present in the structure.
Cross-references: PDB:2XB2
Protein: DP02069 (UniProt P38919)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"The final model includes six bases of polyU RNA, AMPPNP, essentially all of Mago-Y14 (Mago residues 4–146 and Y14 residues 66-154), most of eIF4AIII (except for the 20 N-terminal residues that are disordered)"
Cross-references: PDB:2J0S
Protein: DP02069 (UniProt P38919)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal region of eIF4AIII is disordered, as referenced in Table S2 and confirmed upon visual inspection of the structure.
Cross-references: PDB:5XJC