LiteFold/DisProt huggingface dataset:
Protein: DP03832 (UniProt Q16740)
Region: residues 57	to 72
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6H23
Protein: DP03832 (UniProt Q16740)
Region: residues 250	to 277
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6H23
Protein: DP03833 (UniProt Q9H9E3)
Region: residues 525	to 536
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
The final model includes residues 536–785 of one monomer and 537–785 of the other monomer, with the remaining N-terminal residues, for which no interpretable electron density was observed, likely disordered in the crystals.
Cross-references: PDB:3HR0
Protein: DP03834 (UniProt A4D126)
Region: residues 319	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Residues 55–60, 319–334, and 345–347 are disordered in the electron density map, and not modeled in the final model.
Cross-references: PDB:4CVH
Protein: DP03835 (UniProt P14868)
Region: residues 224	to 247
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, residues 224–247 in the flipping loop and residues 273–282 in the Motif 2 could not be observed in our crystal structure [Fig. 1(B)]. These regions are known to be dynamic without its cognate tRNA and recognize its tRNA in an induced-fit manner.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
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 PDB shows the protein lacks electron density in this region, indicating it is disordered.
In our crystal structure, the C-terminal end of the α-helix in the N-terminal extension was observed, comprising Lys26, Glu27, and Arg28 although the N-terminal region was less-ordered.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
Region: residues 273	to 282
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, residues 224–247 in the flipping loop and residues 273–282 in the Motif 2 could not be observed in our crystal structure [Fig. 1(B)]. These regions are known to be dynamic without its cognate tRNA and recognize its tRNA in an induced-fit manner.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
Region: residues 163	to 172
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The hinge region (residues, 156–188) plays an essential role in the connection of the anticodon-binding domain and the catalytic domain. In the middle of the hinge region, residues 163–172 could not be modeled owing to the lack of the electron density and the disordered residues are considered as a part of binding region to the ribose-phosphate backbone in the D-stem of tRNAAsp, compared with the known S. cerevisiae DRS–tRNAAsp complex structure.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
Region: residues 163	to 172
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, residues 224–247 in the flipping loop and residues 273–282 in the Motif 2 could not be observed in our crystal structure [Fig. 1(B)]. These regions are known to be dynamic without its cognate tRNA and recognize its tRNA in an induced-fit manner.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
Region: residues 237	to 241
Annotation: phosphorylation display site (Disorder function)
Evidence: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
Supporting statements:
Our liquid chromatography tandem mass spectrometry (MS) analysis revealed two phosphorylation sites (Tyr239 and Ser249) and six acetylation sites (Lys55, 110, 213, 241, 330, and 453), respectively.
Cross-references: PDB:4J15
Protein: DP03835 (UniProt P14868)
Region: residues 239	to 243
Annotation: acetylation display site (Disorder function)
Evidence: liquid chromatography coupled with tandem mass spectrometry evidence used in manual assertion
Supporting statements:
Our liquid chromatography tandem mass spectrometry (MS) analysis revealed two phosphorylation sites (Tyr239 and Ser249) and six acetylation sites (Lys55, 110, 213, 241, 330, and 453), respectively.
For instance, although Lys241 was identified with its acetylation modification in our analysis, collected six independent MS analysis data of ubiquitin branch motif (K-e-GG) immunoaffinity beads purification studies showed that Lys241 is also modified with ubiquitin.
Cross-references: PDB:4J15
Protein: DP03836 (UniProt Q6PI48)
Region: residues 631	to 645
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Refinement using a dynamic elastic network (DEN) as implemented in CNS 1.3 (33) led to a reorientation of the insertions and to a dramatic improvement of the electron density map. All residues of HsaDRS2 were built except the 26 C-terminal amino acids (including the 6-His tag), which are disordered.
Cross-references: PDB:4AH6
Protein: DP03837 (UniProt P49366)
Region: residues 76	to 92
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:1DHS
Protein: DP03837 (UniProt P49366)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6P4V
Protein: DP03837 (UniProt P49366)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:6PGR
Protein: DP03838 (UniProt O00548)
Region: residues 443	to 551
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In one copy of Dll-1, residues 21–442 were visible, comprising the C2 domain, DSL domain and EGF-like repeats 1–6 (i.e. missing the last two EGF-like repeats); in the second copy, only the C2, DSL and first two EGF domains were visible (residues 22–291). The two copies of Dll-1 in the asymmetric unit overlay with an RMSD of 2.3 Å.
Cross-references: PDB:4XBM
Protein: DP03839 (UniProt Q92785)
Region: residues 235	to 249
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:3IUF
Protein: DP03841 (UniProt P07814)
Region: residues 1003	to 1014
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:4HVC
Protein: DP03841 (UniProt P07814)
Region: residues 1464	to 1473
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:4HVC
Protein: DP03841 (UniProt P07814)
Region: residues 998	to 1015
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5VAD
Protein: DP03841 (UniProt P07814)
Region: residues 1464	to 1473
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5VAD
Protein: DP03841 (UniProt P07814)
Region: residues 1001	to 1014
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:7OSY
PDB:7OT0
PDB:7OT1
PDB:7OT2
PDB:7OT3
PDB:7OSZ
Protein: DP03842 (UniProt P37268)
Region: residues 315	to 327
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density for residues 315–327 and for the NH2-terminal seven residues was not seen, so they were not included in the final model.
It is also the most flexible part of the structure, indeed residues 315–327 are so disordered that they were not seen in the electron density maps calculated for the CP-320473 structure.
Cross-references: PDB:1EZF
Protein: DP03843 (UniProt Q9BYC5)
Region: residues 68	to 107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As illustrated in Figure 2, the residues of Leu-108 to Glu-572 are modeled, however, the N-terminus (residues 68–107), C-terminus (residues 573–575), and the residues 368–372 are disordered in this structure.
Cross-references: PDB:2DE0
Protein: DP03843 (UniProt Q9BYC5)
Region: residues 41	to 107
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The NH2-terminus (residues 41-107) and the C-terminal residue Lys575 were disordered and left unmodeled.
Cross-references: PDB:6X5H
PDB:6X5T
PDB:6X5R
PDB:6X5U
Protein: DP03845 (UniProt P07902)
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:
There was no interpretable electron density for residues 1–27, 49–63, 367–379 in chain A and residues 1–23, 49–63, 365–379 in chain B.
Cross-references: PDB:5IN3
Protein: DP03845 (UniProt P07902)
Region: residues 49	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 49–63, corresponding to a surface-exposed loop involved in UDP-hexose binding, are disordered in the structure, suggesting its mobility in the absence of this ligand.
There was no interpretable electron density for residues 1–27, 49–63, 367–379 in chain A and residues 1–23, 49–63, 365–379 in chain B.
Cross-references: PDB:5IN3
Protein: DP03845 (UniProt P07902)
Region: residues 367	to 379
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There was no interpretable electron density for residues 1–27, 49–63, 367–379 in chain A and residues 1–23, 49–63, 365–379 in chain B."
Cross-references: PDB:5IN3
Protein: DP03847 (UniProt O94925)
Region: residues 71	to 135
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the N- and C-termini exhibit disorder in this structure, which results in the N-terminal helical domain being flanked by two regions of disordered residues, 71–135 and 547–598.
Cross-references: PDB:3UNW
PDB:3UO9
Protein: DP03847 (UniProt O94925)
Region: residues 72	to 135
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5FI2
PDB:5I94
PDB:5FI7
PDB:5FI6
Protein: DP03847 (UniProt O94925)
Region: residues 646	to 669
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The majority of the C-terminal region of KGA adjacent to the ANK repeats (residues Thr647-Leu669) is likely heterogeneous in conformation and therefore could not be modeled.
Cross-references: PDB:5U0I
PDB:5U0J
Protein: DP03847 (UniProt O94925)
Region: residues 72	to 136
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both structures, only part of the N terminus of GAC is resolved (beginning at Pro-137), and the majority of the C terminus is not visible (ending at Gly-546).
Cross-references: PDB:5WJ6
Protein: DP03848 (UniProt Q9NQX3)
Region: residues 1	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1-12 of Geph-G and residues 459-461 of Cnx1-G are not present in the model and appear to be disordered.
Cross-references: PDB:1JLJ
Protein: DP03849 (UniProt P00492)
Region: residues 104	to 123
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:4KN6
Protein: DP03849 (UniProt P00492)
Region: residues 104	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:4RAB
PDB:4RAC
PDB:4RAN
PDB:4RAQ
Protein: DP03849 (UniProt P00492)
Region: residues 103	to 119
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5BRN
Protein: DP03849 (UniProt P00492)
Region: residues 102	to 121
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows the protein lacks electron density in this region, indicating it is disordered.
Cross-references: PDB:5BSK
Protein: DP03850 (UniProt E9AD06)
Region: residues 1	to 66
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of residues 1-66 is unresolved in the cryo-EM reconstructions, showing its intrinsic flexibility when this protein takes part in the Large subunit from major mitochondrial ribosome.
Cross-references: PDB:7AM2
Protein: DP03851 (UniProt P14678)
Region: residues 90	to 229
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The electron microscopy structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) shows this region of the Small nuclear ribonucleoprotein-associated proteins B and B' lacks electron density, indicating it is disordered.
Cross-references: PDB:6AH0
EMDB:EMD-9621
Protein: DP03851 (UniProt P14678)
Region: residues 50	to 62
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The electron microscopy structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) shows this region of the Small nuclear ribonucleoprotein-associated proteins B and B' lacks electron density, indicating it is disordered.
Cross-references: PDB:6AH0
EMDB:EMD-9621
Protein: DP03851 (UniProt P14678)
Region: residues 92	to 240
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
The electron microscopy structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) shows this region of the Small nuclear ribonucleoprotein-associated proteins B and B' lacks electron density, indicating it is disordered.
Cross-references: EMDB:EMD-4658
PDB:6QW6
PDB:6QX9
EMDB:EMD-4665
Protein: DP03851 (UniProt P14678)
Region: residues 88	to 174
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The X-ray structure of the Human Spliceosomal U1 snRNP shows this region of the Small nuclear ribonucleoprotein-associated proteins B and B' lacks electron density, indicating it is disordered.
Cross-references: PDB:3CW1
Protein: DP03851 (UniProt P14678)
Region: residues 46	to 64
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The X-ray structure of the Human Spliceosomal U1 snRNP shows this region of the Small nuclear ribonucleoprotein-associated proteins B and B' lacks electron density, indicating it is disordered.
Cross-references: PDB:3CW1
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Immediately after removal of Gdn and initiating the aggregation process, the CD spectra of both CsgA and CsgB are characteristic of a random coil with a minimum close to 200 nm and little signal elsewhere.
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In contrast, the CD signal of CsgB rapidly increased at 200 nm and decreased at 216 nm, indicating the appearance of β-sheet structure (Fig. 3B). The CD change of CsgB at either 200 nm or 216 nm could be fit by a single exponential function with a half-time of 180 min (Fig. 3E and Table 1).
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
However, the intrinsic fluorescence of CsgB alone, excited at 280 nm, shows an exponential decrease as a function of time (Fig. 6F) with a rate constant similar to the change in CD signal (Fig. 3E), confirming that the structure of CsgB rapidly changes with a single exponential rate during its aggregation.
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Fig. 1A shows the time dependence for CsgB aggregation as a function of CsgB concentration.
Cross-references: AmyPro:AP00037
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: regulation of amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
Seeds (oligomers) of CsgB abolished the lag phase of CsgA and of CsgB (Fig. 2 A and B). The results suggest that CsgB oligomers accelerate CsgA aggregation.
CsgA is unable to polymerize in the absence of CsgB; thus, in the absence of either CsgA or CsgB, no surface structures are observed (5).
Protein: DP03852 (UniProt P0ABK7)
Region: residues 1	to 151
Annotation: regulation of amyloid fibril formation (Biological process)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In these experiments the CD changes were fit by a two-exponential function (Table 1). Interestingly, the rate constant for the first phase is near that of CsgB alone (Table 1), suggesting that this fast phase is mostly due to the rapid polymerization of CsgB. Thus, it is clear that CsgB rapidly forms oligomers that change the aggregation mechanism of CsgA.
Protein: DP03853 (UniProt P28307)
Region: residues 1	to 151
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Immediately after removal of Gdn and initiating the aggregation process, the CD spectra of both CsgA and CsgB are characteristic of a random coil with a minimum close to 200 nm and little signal elsewhere.
Protein: DP03853 (UniProt P28307)
Region: residues 1	to 151
Annotation: amyloid fibril formation (Biological process)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The effect of monomeric CsgB on the aggregation of CsgA was investigated using the ThT assay. A 1:1 mixture of monomeric CsgA and CsgB (4 μM each) was observed to have a lag phase similar to that of CsgB alone over the first 100 min (Fig. 1B). Thus, the lag phase typical of CsgA alone disappeared (Fig. 1B). 
The intrinsic fluorescence of CsgA alone, excited at 280 nm, shows a small linear decrease over time, monitored by either tyrosine or tryptophan signal (Fig. 6E), which is probably due to the loss of soluble protein during the aggregation process.
Cross-references: AmyPro:AP00036
Protein: DP03853 (UniProt P28307)
Region: residues 1	to 151
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
At very long times (9–13 d), the CD spectrum of CsgA shows a weak minimum signal at ~220 nm, rather than at 216 nm, but probably characteristic of some β-sheet structures (Fig. 3 C and D).
Protein: DP03853 (UniProt P28307)
Region: residues 1	to 151
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Immediately after elution from the nitrilotriacetic acid (NTA) agarose column, solutions containing purified CsgA-his were clear with no evidence of aggregation, and EM of this material revealed no fibers (9). CD analysis of this material indicated that soluble CsgA-his, unlike curli, was not rich in β-sheet secondary structure (Fig. 4C).