LiteFold/DisProt huggingface dataset:
Protein: DP02825 (UniProt P31153)
Region: residues 117	to 129
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure lacked  substrates  or  products;  therefore,  the  Mat2A  gating  loop (Mat2A residues 109–140), which closes upon substrate binding, was disordered and not observed.
Numbering is referred to chain A of the PDB
Cross-references: PDB:5UGH
Protein: DP02826 (UniProt P40344)
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 20 amino-terminal and 4 carboxyl-terminal residues as well as three regions corresponding to residues 84–128, 143–162, and 271–278 lacked defined electron density and were omitted from the model.
Cross-references: PDB:2DYT
Protein: DP02826 (UniProt P40344)
Region: residues 84	to 128
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 20 amino-terminal and 4 carboxyl-terminal residues as well as three regions corresponding to residues 84–128, 143–162, and 271–278 lacked defined electron density and were omitted from the model.
Cross-references: PDB:2DYT
Protein: DP02826 (UniProt P40344)
Region: residues 143	to 162
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 20 amino-terminal and 4 carboxyl-terminal residues as well as three regions corresponding to residues 84–128, 143–162, and 271–278 lacked defined electron density and were omitted from the model.
Cross-references: PDB:2DYT
Protein: DP02826 (UniProt P40344)
Region: residues 84	to 162
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Because most residues of FR are disordered in the crystal, we could not obtain further structural information on FR from the crystal structure.To obtain structural information on FR in solution, we expressed the FR moiety of Atg3 (83–162) in E. coli, purified it,and analyzed it by NMR spectroscopy. Fig. 3A shows the 1H-15N HSQC spectrum of the FR moiety of Atg3.
Intriguingly, the spectrum of full-length Atg3 was strikingly similar to that of FR, suggesting that most observed signals for full-length Atg3 were derived from the FR moiety. This observation indicates that the mobility of FR is much higher than that of other regions of Atg3 because the residues located at the flexible regions give strong NMR signals because of long T2 relaxation times compared with those located at the rigid regions.
These results suggest that the FR moiety of Atg3 has a random coil structure and is highly mobile in solution, not only in the isolated state but also in intact Atg3. Although residues 129–142 of FR have a helical structure in the crystal (Fig. 1,A and B), they may have a more flexible conformation in solution.
Protein: DP02826 (UniProt P40344)
Region: residues 84	to 162
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Furthermore,in vitro pull down assays showed that FR of Atg3 mediated the binding of Atg7.
Protein: DP02826 (UniProt P40344)
Region: residues 129	to 142
Annotation: molten globule (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The conformation of residues 129–142, which are modeled as helix C, also seems to be flexible because the average B-factor of these residues is rather high (89.9 and 54.0 Å2 for helix C and all Atg3 residues, respectively). 
Cross-references: PDB:2DYT
Protein: DP02826 (UniProt P40344)
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:
Otherwise, several loops in Atg7, Atg3, and Atg10, and the BMOE crosslink not visible in the electron density were not modeled in the structures.
Cross-references: PDB:4GSL
Protein: DP02826 (UniProt P40344)
Region: residues 84	to 128
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Otherwise, several loops in Atg7, Atg3, and Atg10, and the BMOE crosslink not visible in the electron density were not modeled in the structures.
In both the free and Atg7-bound Atg3 structures, the majority of the FR is disordered, except for a small helical segment.
Cross-references: PDB:4GSL
Protein: DP02826 (UniProt P40344)
Region: residues 142	to 162
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Otherwise, several loops in Atg7, Atg3, and Atg10, and the BMOE crosslink not visible in the electron density were not modeled in the structures.
In both the free and Atg7-bound Atg3 structures, the majority of the FR is disordered, except for a small helical segment.
Cross-references: PDB:4GSL
Protein: DP02826 (UniProt P40344)
Region: residues 247	to 280
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Otherwise, several loops in Atg7, Atg3, and Atg10, and the BMOE crosslink not visible in the electron density were not modeled in the structures.
IDR inside the ‘handle region’ (HR) of Atg3.
Cross-references: PDB:4GSL
Protein: DP02826 (UniProt P40344)
Region: residues 270	to 273
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we show by NMR spectroscopy that Atg3 directly interacts with Atg8 through the WEDL sequence in HR and that the interaction is quite similar to Atg8-Atg19AIM and LC3-p62AIM interactions. Thus, the WEDL sequence of Atg3 is a canonical AIM.
The region includes the canonical LIR motif "WEDL".
Protein: DP02826 (UniProt P40344)
Region: residues 270	to 273
Annotation: selective autophagy (Biological process)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here, we show by NMR spectroscopy that Atg3 directly interacts with Atg8 through the WEDL sequence in HR and that the interaction is quite similar to Atg8-Atg19AIM and LC3-p62AIM interactions. Thus, the WEDL sequence of Atg3 is a canonical AIM.
The region includes the canonical LIR motif "WEDL".
Protein: DP02826 (UniProt P40344)
Region: residues 82	to 165
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
As expected, the log(Rh) vs. log(Mw) dependency for Atg3FR was significantly displaced from the linear dependency log(Rh) vs. log(Mw) of standard globular proteins, and its experimental hydrodynamic radius exceeds the calculated hydrodynamic radius of both a native-coil-like IDP and a GdmCl-unfolded globular protein with comparable molecular mass (Table 1). This suggests that Atg3FR adopts a conformation even more disordered than that of the full-length Atg3.
Protein: DP02826 (UniProt P40344)
Region: residues 82	to 165
Annotation: disorder (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
 In comparison, the far-UV CD spectrum of Atg3FR (Fig. 3B) did resemble the spectrum of unordered structures with a negative minimum at approximately 200 nm,38,39 indicating that the secondary structure is missing in Atg3FR.
Protein: DP02826 (UniProt P40344)
Region: residues 82	to 165
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Atg3FR, which behaved as an extended random-coil-like protein (Fig. 2; Fig. 3), has a predicted molecular mass of 10 kDa, but migrated at the position of a polypeptide twice as large (Fig. 4A; Table 2).
Protein: DP02827 (UniProt P22523)
Region: residues 59	to 76
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The second helix H2 is connected to strand S3 by a long, mostly flexible loop. Residues 59 to 76 are disordered in the crystal.
Cross-references: PDB:1QHL
Protein: DP02828 (UniProt Q9W058)
Region: residues 281	to 291
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 250–­257 in the hydrophilic linker, which is absent in the bacterial homologues, are invisible in the electron-density maps. The region consisting of residues 373–383 is also disordered in the DmSCOT structure.
Residue numbering reported by the authors of the publication refers to the PDB structure. The interdomain flexible linker corresponds to region 281-291.
Cross-references: PDB:4KGB
Protein: DP02828 (UniProt Q9W058)
Region: residues 281	to 291
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 250–­257 in the hydrophilic linker, which is absent in the bacterial homologues, are invisible in the electron-density maps. The region consisting of residues 373–383 is also disordered in the DmSCOT structure.
Residue numbering reported by the authors of the publication refers to the PDB structure. The interdomain flexible linker corresponds to region 281-291.
Protein: DP02829 (UniProt P46379)
Region: residues 1057	to 1112
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The x-ray crystal structure of the complex was determined at 1.85 Å resolution. Unambiguous electron density allowed modeling of residues 1058–1112 of BAG6 BAGS and 94–143 of Ubl4a TUGS.
Cross-references: PDB:4X86
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The x-ray crystal structure of the complex was determined at 1.85 Å resolution. Unambiguous electron density allowed modeling of residues 1058–1112 of BAG6 BAGS and 94–143 of Ubl4a TUGS.
Cross-references: PDB:4X86
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On the other hand, the profile of BAG6 BAGS exhibited a large negative value at 200 nm but a small negative value at 222 nm, suggesting that it is almost unstructured; the α-helical content was estimated as 14% from the value at 222 nm.
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
When BAG6 BAGS and Ubl4a were mixed, the profile revealed a typical α-helical structure whose intensity was greater than that of Ubl4a or BAG6 BAGS alone; the α-helical content was estimated to be 38% from the value at 222 nm. The secondary structure content was calculated using the K2D3 software (31). The α-helix and β-sheet contents were estimated to be 26 and 18% (Ubl4a), 19 and 16% (BAG6 BAGS), and 43 and 10% (BAG6 BAGS + Ubl4a), respectively. Thus, α-helical content increased upon complex formation. The change in β-sheet content was smaller than the change in α-helical content, and β-sheet contents were less than 20% in all cases. Thus, we suspect that the BAG6 BAGS fragment is disordered and/or non-helical in its monomeric form but forms helical structures upon Ubl4a binding.
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
We used SAXS to show that the BAG6 BAGS-Ubl4a TUGS complex exists as a heterodimer in solution.
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: molecular function activator activity (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Furthermore, the tight association of BAG6 and Ubl4a resulted in modulation of Ubl4a protein stability in cells. 
The structure of Ubl4a, which interacts with BAG6, is similar to the yeast homologue Get5, which forms a homodimer. These observations indicate that the BAGS domain of BAG6 promotes the TA protein biogenesis pathway in mammals by the interaction with Ubl4a.
BAG6 association stabilizes the Ubl4a protein. A, Ubl4a protein is destabilized by loss of its C-terminal BAG6 binding region.
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In this study, we obtained evidence that the C terminus of BAG6 (previously designated as a BAG domain) is essential for tethering the C-terminal conserved stretch of Ubl4a, designated here as the TUGS (tethering Ubl4a to BAGS) domain.
Protein: DP02829 (UniProt P46379)
Region: residues 1048	to 1123
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Using the bacterially expressed BAGS domain of BAG6 (residues 1048–1123) and the C-terminal region of Ubl4a (residues 95–147), we characterized the BAG6-Ubl4a interaction. To measure the affinity between BAG6 BAGS and Ubl4a TUGS, we carried out SPR experiments (Fig. 3A). Surprisingly, the calculated overall dissociation constant was very small, 2.2 ± 0.5 nm, suggesting that these two proteins form a very tight complex.
Protein: DP02829 (UniProt P46379)
Region: residues 395	to 1029
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
The protein structure of BAG6/BAT3 can be subdivided in three parts: a N-terminal region (aa1–aa474) comprising an ubiquitin-like domain (UBL, aa13–aa87), a central domain comprising a long disordered Pro-rich domain (aa395–aa1029) bearing short polyPro and polyGly sequences which may be involved in inter- and intramolecular protein–protein interactions, a zinc-finger domain (aa851–aa884) and a C-terminal region (aa1030–aa1132), comprising the nuclear localization sequence (NLS, aa1030–aa1055), and the BAG domain (aa1000–aa1111).
Protein: DP02830 (UniProt Q91YD9)
Region: residues 419	to 428
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The limitations, however, are that individual atomic positions cannot be refined and the inter-W linkers cannot be visualized.
Flexible linker connecting WH2 1 domain and WH2 2 domain.
Cross-references: PDB:3M3N
Protein: DP02830 (UniProt Q91YD9)
Region: residues 419	to 428
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The limitations, however, are that individual atomic positions cannot be refined and the inter-W linkers cannot be visualized.
Flexible linker connecting WH2 1 domain and WH2 2 domain.
Cross-references: PDB:3M3N
Protein: DP02831 (UniProt Q13164)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ERK5 residues 47–393 were resolved in the electron density with the exception of the activation loop residues 208–214, which were disordered (Figure ​1), and residues 288–292, which form a short loop in the CMGC-specific insert. In o
Cross-references: PDB:4B99
Protein: DP02831 (UniProt Q13164)
Region: residues 1	to 46
Annotation: localization (Biological process)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
ERK5 residues 47–393 were resolved in the electron density with the exception of the activation loop residues 208–214, which were disordered (Figure ​1), and residues 288–292, which form a short loop in the CMGC-specific insert. In o
The region N-terminal to the kinase domain contains sequences for targeting to the cytoplasm, while in the C-terminal region there is a nuclear localization sequence (residues 505–539). ERK5 is found in both cytoplasmic and nuclear locations.
Cross-references: PDB:4B99
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 492	to 545
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density not visible for the residues between the two regions involved in cofactor (SAM/SAH) binding 
Cross-references: PDB:6DCB
PDB:6DCC
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 400	to 689
Annotation: RNA binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
MePCE binds tightly to capped RNA.
5′ capping is a tightly regulated step in RNA processing that is required for RNA stability, localization, and function.
The MePCE region used for ITC experiments corresponds to MTase domain (residues 400–689)
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 400	to 689
Annotation: molecular function regulator (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
MePCE binds tightly to capped RNA.
5′ capping is a tightly regulated step in RNA processing that is required for RNA stability, localization, and function.
The MePCE region used for ITC experiments corresponds to MTase domain (residues 400–689)
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 418	to 431
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle.
Based on studies indicating that MePCE binds the proximal end of the 7SK SL1 and adjacent ssRNA in vivo (Fig. 1c), we designed and synthesized an RNA hairpin-ssRNA construct comprising the 5′-end of 7SK SL1 with a UUCG tetraloop and an eight nucleotide ssRNA 3′ overhang (SL1p).
The structures of MePCE–SAH in the absence and presence of SL1p are globally similar (all atom RMSD 0.29 Å), but there are major differences around the active site and RNA-protein interface (Fig. 2e,f). In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle (Fig. 2b,e).
Authors of the publication compare their crystal structures of MePCE-MT bound to SL1p (PDB: 6dcb, 6dcc) to an unpublished structure of unbound MePCE-MT (PDB:5UNA), to highlights the conformational changes in MePCEMT that occur on RNA binding.
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 418	to 431
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle.
Based on studies indicating that MePCE binds the proximal end of the 7SK SL1 and adjacent ssRNA in vivo (Fig. 1c), we designed and synthesized an RNA hairpin-ssRNA construct comprising the 5′-end of 7SK SL1 with a UUCG tetraloop and an eight nucleotide ssRNA 3′ overhang (SL1p).
The structures of MePCE–SAH in the absence and presence of SL1p are globally similar (all atom RMSD 0.29 Å), but there are major differences around the active site and RNA-protein interface (Fig. 2e,f). In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle (Fig. 2b,e).
Authors of the publication compare their crystal structures of MePCE-MT bound to SL1p (PDB: 6dcb, 6dcc) to an unpublished structure of unbound MePCE-MT (PDB:5UNA), to highlights the conformational changes in MePCEMT that occur on RNA binding.
Cross-references: PDB:6DCB
PDB:6DCC
Protein: DP02832 (UniProt Q7L2J0)
Region: residues 665	to 676
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle.
Based on studies indicating that MePCE binds the proximal end of the 7SK SL1 and adjacent ssRNA in vivo (Fig. 1c), we designed and synthesized an RNA hairpin-ssRNA construct comprising the 5′-end of 7SK SL1 with a UUCG tetraloop and an eight nucleotide ssRNA 3′ overhang (SL1p).
The structures of MePCE–SAH in the absence and presence of SL1p are globally similar (all atom RMSD 0.29 Å), but there are major differences around the active site and RNA-protein interface (Fig. 2e,f). In the absence of RNA, the N-terminus (residues 418–431) and C-terminal β6-β7 loop (residues 665–676) are partially disordered (Fig. 2c,f), while in the presence of meSL1p, a helix α0 forms near the N-terminus, loop residues that connect to α1 become ordered, and the β6-β7 loop adopts an ordered structure with a short helix α7 in the middle (Fig. 2b,e).
Authors of the publication compare their crystal structures of MePCE-MT bound to SL1p (PDB: 6dcb, 6dcc) to an unpublished structure of unbound MePCE-MT (PDB:5UNA), to highlights the conformational changes in MePCEMT that occur on RNA binding.
Cross-references: PDB:6DCB
PDB:6DCC