LiteFold/DisProt huggingface dataset:
Protein: DP04078 (UniProt P35790-2)
Region: residues 131	to 140
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB structure 2CKO shows that this region is ordered, compared to PDB 2CKP (hCKADP) which presents the lack of traceable electron density described in evidence DP04078r004.
Cross-references: PDB:2CKO
Protein: DP04078 (UniProt P35790-2)
Region: residues 131	to 140
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that a lack of traceable electron density in some regions of the hCKADP structure prevented us from modelling ~25% of the residues in comparison to the apo-structure. Specifically, residues 131–139, 149–175 (missing insertion in all pdbs), 262–268, 314–326 in chain A; 87–91, 118–121, 131–141, 148–176, 256–277, 317–323, 388–389, 424–440 in chain B.
Cross-references: PDB:2CKP
Protein: DP04078 (UniProt P35790-2)
Region: residues 131	to 140
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that a lack of traceable electron density in some regions of the hCKADP structure prevented us from modelling ~25% of the residues in comparison to the apo-structure. Specifically, residues 131–139, 149–175 (missing insertion in all pdbs), 262–268, 314–326 in chain A; 87–91, 118–121, 131–141, 148–176, 256–277, 317–323, 388–389, 424–440 in chain B.
The region gets disordered when the protein interacts with ADP.
Cross-references: PDB:2CKP
PDB:2CKO
Protein: DP04078 (UniProt P35790-2)
Region: residues 296	to 308
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that a lack of traceable electron density in some regions of the hCKADP structure prevented us from modelling ~25% of the residues in comparison to the apo-structure. Specifically, residues 131–139, 149–175 (missing insertion in all pdbs), 262–268, 314–326 in chain A; 87–91, 118–121, 131–141, 148–176, 256–277, 317–323, 388–389, 424–440 in chain B.
The region 314-326 mentioned by the author corresponds to residues 296-308 of this isoform.
Cross-references: PDB:2CKP
Protein: DP04078 (UniProt P35790-2)
Region: residues 296	to 308
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDB structure 2CKO shows that this region is ordered, compared to PDB 2CKP (hCKADP) which presents the lack of traceable electron density described in evidence DP04078r006.
The region 314-326 mentioned by the author corresponds to residues 296-308 of this isoform.
Cross-references: PDB:2CKO
Protein: DP04078 (UniProt P35790-2)
Region: residues 296	to 308
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that a lack of traceable electron density in some regions of the hCKADP structure prevented us from modelling ~25% of the residues in comparison to the apo-structure. Specifically, residues 131–139, 149–175 (missing insertion in all pdbs), 262–268, 314–326 in chain A; 87–91, 118–121, 131–141, 148–176, 256–277, 317–323, 388–389, 424–440 in chain B.
The region gets disordered when the protein interacts with ADP.
The region 314-326 mentioned by the author corresponds to residues 296-308 of this isoform.
Cross-references: PDB:2CKO
PDB:2CKP
Protein: DP04080 (UniProt Q9ULK4)
Region: residues 1335	to 1368
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model is complete, with the exception of the last 30 residues, which have no visible electron density.
Cross-references: PDB:6H02
Protein: DP04081 (UniProt Q9UIW2)
Region: residues 25	to 38
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Missing residues (residues 25–38 in Plexin-A1, and residues 19–22, 47–54, 479–483, 545–553, and 569–570 in Sema6D) were added using MODELLER.
Cross-references: PDB:7Y4P
Protein: DP04082 (UniProt Q9NXG6)
Region: residues 88	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first visible P4H-TM residues are Thr107 and Leu108 in chains A and B, respectively. Including the 6xHis tag, there are 25 disordered residues in the N-terminus that are not visible in the electron density.
Cross-references: PDB:6TP5
Protein: DP04082 (UniProt Q9NXG6)
Region: residues 482	to 502
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 21 residues of P4H-TM are not visible in the electron density.
Cross-references: PDB:6TP5
Protein: DP04083 (UniProt Q9BPU6)
Region: residues 493	to 564
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For WT CRMP-5, residues 1–6, 492–564, and 1–7, 493–564 of chains A and B, respectively, as well as all 23 residues added to the N-termini by the cloning procedure could not be traced.
Cross-references: PDB:4B90
Protein: DP04084 (UniProt P37093)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the N-terminal 13 residues and the C-terminal 15 residues of N1-EpsE had no representative electron density and most are likely disordered in the crystal.
Cross-references: PDB:2BH1
Protein: DP04084 (UniProt P37093)
Region: residues 82	to 96
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the N-terminal 13 residues and the C-terminal 15 residues of N1-EpsE had no representative electron density and most are likely disordered in the crystal.
Cross-references: PDB:2BH1
Protein: DP04086 (UniProt P54577)
Region: residues 343	to 364
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The three N-terminal amino acids and 22 residues from Asp-343 to Ile-364 were disordered.
Cross-references: PDB:1N3L
Protein: DP04086 (UniProt P54577)
Region: residues 343	to 364
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This disordered segment is the linker that joins the 169-aa, EMAP II-like C domain of native TyrRS to the body of the enzyme (mini-TyrRS).
Cross-references: PDB:1N3L
Protein: DP04087 (UniProt P07206)
Region: residues 21	to 38
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 19-residue N-terminal tether or linker, which connects the lipid anchor with the structured parts of the protein, was completely disordered and invisible in the structure, although its presence in purified PulANA was confirmed by Edman degradation.
Cross-references: PDB:2YOC
Protein: DP04087 (UniProt P07206)
Region: residues 21	to 38
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The 19-residue N-terminal tether or linker, which connects the lipid anchor with the structured parts of the protein, was completely disordered and invisible in the structure, although its presence in purified PulANA was confirmed by Edman degradation.
Cross-references: PDB:2YOC
Protein: DP04088 (UniProt Q7Y3F1)
Region: residues 289	to 308
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linker regions between the central helical bundle and the two terminal domains showed partial disorder in electron density, consistent with limited proteolysis data that demonstrated that both domains could be readily dissociated from the holoenzyme.
The Cα atoms of the model show the N-terminal residues 1–205 in light blue, the disordered linker 1 (residues 206–227) in red, the helical structure (residues 226–288) that docks PlyCA to PlyCB in yellow, the second disordered linker 2 (residues 289–308) in a dashed red line, and the CHAP domain (residues 309–465) in green.
Cross-references: PDB:4F88
Protein: DP04088 (UniProt Q7Y3F1)
Region: residues 289	to 308
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Linker regions between the central helical bundle and the two terminal domains showed partial disorder in electron density, consistent with limited proteolysis data that demonstrated that both domains could be readily dissociated from the holoenzyme.
The Cα atoms of the model show the N-terminal residues 1–205 in light blue, the disordered linker 1 (residues 206–227) in red, the helical structure (residues 226–288) that docks PlyCA to PlyCB in yellow, the second disordered linker 2 (residues 289–308) in a dashed red line, and the CHAP domain (residues 309–465) in green.
Cross-references: PDB:4F88
Protein: DP04089 (UniProt P0AGD7)
Region: residues 341	to 368
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Despite the presence of RNA, however, a 33-amino acid residue segment (338–370) within the M-domain was disordered within the original co-crystal structure (Batey et al., 2000).
Cross-references: PDB:1HQ1
Protein: DP04090 (UniProt P26949)
Region: residues 23	to 39
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit contains four Caf1AN molecules
with very similar structures. None of the molecules have electron
density for the N- and C-terminal parts of Caf1AN before Asp18
and after Phe124, respectively, suggesting that these sequences
are not structured in Caf1AN.
Cross-references: PDB:4B0E
Protein: DP04090 (UniProt P26949)
Region: residues 23	to 39
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures of Caf1M:Caf1 and the core of Caf1AN remain
essentially unchanged after binding. The largest conformational
change occurs in the N-terminal 1-17 amino acid sequence of
Caf1AN, which becomes ordered in Caf1AN:Caf1M:Caf1 (Figure
2A; Figure S1E).
Cross-references: PDB:4B0E
PDB:4B0M
Protein: DP04090 (UniProt P26949)
Region: residues 145	to 158
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The asymmetric unit contains four Caf1AN molecules
with very similar structures. None of the molecules have electron
density for the N- and C-terminal parts of Caf1AN before Asp18
and after Phe124, respectively, suggesting that these sequences
are not structured in Caf1AN.
Cross-references: PDB:4B0E
Protein: DP04091 (UniProt P26926)
Region: residues 130	to 145
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered part of the F1G1 loop in Caf1M (not observed in crystal structures) is indicated with a dashed line.
Cross-references: PDB:4B0M
Protein: DP04092 (UniProt P02710)
Region: residues 205	to 222
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
From the HSQC titration, it is clear that the free peptide (Fig. 2 A) is largely unstructured.
Protein: DP04092 (UniProt P02710)
Region: residues 205	to 222
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to Cbtx, the chemical shift positions of the HN resonances for the bound peptide are altered due to complex formation but remain fixed in position and do not vary as a function of the Cbtx concentration (Fig. 2, B–D).
Cross-references: PDB:1LXG
PDB:1LXH
Protein: DP04092 (UniProt P02710)
Region: residues 205	to 222
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Upon binding to Cbtx, the chemical shift positions of the HN resonances for the bound peptide are altered due to complex formation but remain fixed in position and do not vary as a function of the Cbtx concentration (Fig. 2, B–D).
Cross-references: PDB:1LXG
PDB:1LXH
Protein: DP04092 (UniProt P02710)
Region: residues 356	to 393
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The PDB of the cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-bungarotoxin shows this region lacks electron density, indicating it is disordered. 
Cross-references: EMDB:20928
PDB:6UWZ
Protein: DP04093 (UniProt P30531)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although a full-length construct of human GAT1 was used for structure determination, the N terminus (residues 1–46) and C terminus (residues 578–599) are disordered and were not observed in our reconstruction.
Cross-references: PDB:7SK2
Protein: DP04093 (UniProt P30531)
Region: residues 578	to 599
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although a full-length construct of human GAT1 was used for structure determination, the N terminus (residues 1–46) and C terminus (residues 578–599) are disordered and were not observed in our reconstruction.
Cross-references: PDB:7SK2
Protein: DP04094 (UniProt P35219)
Region: residues 1	to 22
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 23 residues were not observed in the electron density map and are presumably disordered.
Cross-references: PDB:2W2J
Protein: DP04095 (UniProt P49758)
Region: residues 453	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 that the protein lacks electron density in this region, indicating it is disordered at the C-terminal.
Cross-references: PDB:2ES0
Protein: DP04096 (UniProt A0A0B4JDC9)
Region: residues 909	to 935
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A structural cartoon representation of molecule “B” of the three FN-III domains in RIM-BP. Linker regions are colored in sand and β-strands in red, and unmodeled linker regions are indicated by dashed lines. 
Cross-references: PDB:6Q9M
Protein: DP04096 (UniProt A0A0B4JDC9)
Region: residues 909	to 935
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A structural cartoon representation of molecule “B” of the three FN-III domains in RIM-BP. Linker regions are colored in sand and β-strands in red, and unmodeled linker regions are indicated by dashed lines.
Cross-references: PDB:6Q9M
Protein: DP04097 (UniProt P46097)
Region: residues 8	to 41
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The remainder of the fused Syt-II was disordered and not visible in the electron density. The asymmetric unit contained two BoNT/B molecules, which were virtually identical (r.m.s.d. of 0.4 Å).
Cross-references: PDB:4KBB
Protein: DP04098 (UniProt P49802)
Region: residues 451	to 463
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows that the protein lacks electron density in this region, indicating it is disordered at the C-terminal.
Cross-references: PDB:2A72
Protein: DP04098 (UniProt P49802)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the class C orphan GPCR GPR158 (Q5T848) in complex with RGS7(P49802)-Gβ5(O14775) shows that this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:7EWP
EMDB:31360
PDB:7EWR
EMDB:31363
Protein: DP04098 (UniProt P49802)
Region: residues 219	to 255
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both complexes, structures of GPR158 and the four domains of RGS7 DEP (Dishevelled, Egl10, Pleckstrin), DHEX (DEP helical extension), GGL linker, and the RGS domain, and the Gβ5 subunit were clearly visible and their models fitted well into the cryo-EM maps (Supplementary Fig. 9o, p).
The electron microscopy of the class C orphan GPCR GPR158 (Q5T848) in complex with RGS7(P49802)-Gβ5(O14775) shows that this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:7EWP
EMDB:31360
PDB:7EWR
EMDB:31363
Protein: DP04098 (UniProt P49802)
Region: residues 451	to 495
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy of the class C orphan GPCR GPR158 (Q5T848) in complex with RGS7(P49802)-Gβ5(O14775) shows that this protein region lacks electron density, indicating it is disordered.
Cross-references: PDB:7EWP
EMDB:31360
PDB:7EWR
EMDB:31363
Protein: DP04100 (UniProt O00584)
Region: residues 215	to 234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No model could be built for residues 188–192 and 214–235 as well as the terminal ends as they were disordered.
Cross-references: PDB:3T0O
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 1	to 11
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Here, we have characterized SMG-9, showing that it comprises an N-terminal 180 residue intrinsically disordered region (IDR) followed by a well-folded C-terminal domain.
The N-terminal domain is an intrinsically disordered region (IDR) essential for the maintenance of the structural integrity of the SMG-1:SMG-8:SMG-9 complex.
In standard conditions, GST-NT-SMG-9 was expressed as a soluble protein, but 20–30% of the recovered protein from the GST column was non-specifically proteolysed. We identified the non-specific cleavage site by sequencing of the N-terminus and by mass spectrometry of the spontaneous truncated product. We found that the first 11 amino acids of NT-SMG-9 were removed non-specifically during purification and we therefore recloned the fragment without these residues in the GST vector to produce a more stable product. This construct, GST-NT-SMG-912–180, missing the first 11 amino acids, expressed as a soluble protein and was entirely stable after performing the purification steps described earlier (Figure 2A).
Here, we show that SMG-9 comprises an N-terminal domain with the characteristic features of the so-called intrinsically disordered regions (IDRs) and a well-folded C-terminal domain (12).
Protein: DP04101 (UniProt Q9H0W8)
Region: residues 12	to 180
Annotation: pre-molten globule (Structural state)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Here, we have characterized SMG-9, showing that it comprises an N-terminal 180 residue intrinsically disordered region (IDR) followed by a well-folded C-terminal domain.
The N-terminal domain is an intrinsically disordered region (IDR) essential for the maintenance of the structural integrity of the SMG-1:SMG-8:SMG-9 complex.
Whereas completely unfolded polypeptides are characterized by a well-defined CD spectrum with a minimum in the vicinity of 200 nm and an ellipticity close to zero in the vicinity of 222 nm, the CD-spectra of NT-SMG-912–180 showed a minimum at 205 nm and negative values of ellipticity from ∼235 to 200 nm (Figure 3A). This suggested the presence of certain content in secondary structure.
Here, we show that SMG-9 comprises an N-terminal domain with the characteristic features of the so-called intrinsically disordered regions (IDRs) and a well-folded C-terminal domain (12).
We have purified a protein comprising the N-terminal domain and several biophysical approaches (gel filtration chromatography, analytical ultracentrifugation, CD, and UV-spectroscopy) have confirmed unambiguously that this region behaves as a compact 20 kDa domain with the paradigmatic characteristics of unstructured domains as well as a limited presence of secondary structure.
Furthermore, the combination of NMR data and the spectroscopy studies suggests that the conformation of the NT-SMG-9 domain most likely fits into the category of intrinsically unstructured proteins termed ‘pre-molten globules’, where a limited degree of secondary structure could be localized.