LiteFold/DisProt huggingface dataset:
Protein: DP02518 (UniProt Q8ZRW0)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Mass spectrometry confirmed the N-terminal LptD 24–224 amino acids and LptE residues 170–196 were removed by α-chymotrypsin
Protein: DP02518 (UniProt Q8ZRW0)
Region: residues 24	to 224
Annotation: disorder (Structural state)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
Mass spectrometry confirmed the N-terminal LptD 24–224 amino acids and LptE residues 170–196 were removed by α-chymotrypsin
Protein: DP02518 (UniProt Q8ZRW0)
Region: residues 170	to 196
Annotation: disorder (Structural state)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
Mass spectrometry confirmed the N-terminal LptD 24–224 amino acids and LptE residues 170–196 were removed by α-chymotrypsin
Protein: DP02518 (UniProt Q8ZRW0)
Region: residues 170	to 196
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Mass spectrometry confirmed the N-terminal LptD 24–224 amino acids and LptE residues 170–196 were removed by α-chymotrypsin
Protein: DP02519 (UniProt Q01080)
Region: residues 115	to 415
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal A49 tWH domain and several other regions are disordered and could not be modelled
A49 tWH domain seems to be mobile in all three crystal forms and thus cannot be modelled
Cross-references: PDB:4C3J
PDB:4C3H
PDB:4C3I
Protein: DP02519 (UniProt Q01080)
Region: residues 116	to 415
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density revealed the downstream DNA, the DNA–RNA hybrid (Fig. 1b), and all Pol I domains with the exception of the flexibly linked C-terminal domain of subunit A49
Cross-references: PDB:5M3F
PDB:5M3M
Protein: DP02519 (UniProt Q01080)
Region: residues 115	to 415
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
the C-terminal tandem winged helix domain (tWH) of A49 was absent in the complex.
A49 tWH and A12.2 C-Terminal Domains Are Mobile Elements
Cross-references: PDB:5M5W
PDB:5M5X
Protein: DP02519 (UniProt Q01080)
Region: residues 115	to 415
Annotation: DNA binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
the C-terminal tandem winged helix domain (tWH) of A49 was absent in the complex.
Binding of the tWH to the upstream DNA could stabilize its interaction with the protrusion domain and enforce a closed clamp, thereby enhancing processivity.
Protein: DP02519 (UniProt Q01080)
Region: residues 182	to 403
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
Pol I Transition upon DNA Binding
Protein: DP02519 (UniProt Q01080)
Region: residues 115	to 415
Annotation: molecular function regulator (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
the C-terminal tandem winged helix domain (tWH) of A49 was absent in the complex.
Binding of the tWH to the upstream DNA could stabilize its interaction with the protrusion domain and enforce a closed clamp, thereby enhancing processivity.
Cross-references: PDB:5M5X
Protein: DP02520 (UniProt G0S3L5)
Region: residues 1114	to 1185
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1,114–1,185, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were disordered in both crystal forms and are not included in the models.
construct CthCD-CTCter (1,114–2,297)
Cross-references: PDB:5I6F
PDB:5I6G
Protein: DP02520 (UniProt G0S3L5)
Region: residues 1213	to 1252
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1,114–1,185, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were disordered in both crystal forms and are not included in the models.
Residues 1,033–1,035, 1,134–1,152, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were not included in the models.
In addition, residues 1,032–1,039, 1,134–1,152, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were not included in the model.
construct CthCD-CTCter (1,114–2,297, PDB:516F and 516G), construct CthCD-CT (788–2,297, PDB:5I6H) and construct CthΔBCCP (1–2,297, Δ700–765, PDB:5I6I)
Cross-references: PDB:5I6F
PDB:5I6G
PDB:5I6H
PDB:5I6I
Protein: DP02520 (UniProt G0S3L5)
Region: residues 1134	to 1152
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1,033–1,035, 1,134–1,152, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were not included in the models.
In addition, residues 1,032–1,039, 1,134–1,152, 1,213–1,252, 1,380–1,385, 1,465–1,468 and 2,188–2,195 were not included in the model.
construct CthCD-CT (788–2,297, PDB:5I6H) and construct CthΔBCCP (1–2,297, Δ700–765, PDB:5I6I)
Cross-references: PDB:5I6H
Protein: DP02520 (UniProt G0S3L5)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
To improve crystallizability, we generated ΔBCCP variants of full-length ACC, which, based on SAXS analysis, preserve properties of intact ACC (Supplementary Table 1 and Supplementary Fig. 2a–c). For CthΔBCCP, crystals diffracting to 8.4 Å resolution were obtained. However, molecular replacement did not reveal a unique positioning of the BC domain. Owing to the limited resolution the discussion of structures of CthCD-CT and CthΔBCCP is restricted to the analysis of domain localization. Still, these structures contribute considerably to the visualization of an intrinsically dynamic fungal ACC.
Cross-references: PDB:5I6I
Protein: DP02520 (UniProt G0S3L5)
Region: residues 1	to 699
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
To improve crystallizability, we generated ΔBCCP variants of full-length ACC, which, based on SAXS analysis, preserve properties of intact ACC (Supplementary Table 1 and Supplementary Fig. 2a–c). For CthΔBCCP, crystals diffracting to 8.4 Å resolution were obtained. However, molecular replacement did not reveal a unique positioning of the BC domain. Owing to the limited resolution the discussion of structures of CthCD-CT and CthΔBCCP is restricted to the analysis of domain localization. Still, these structures contribute considerably to the visualization of an intrinsically dynamic fungal ACC.
Cross-references: PDB:5I6I
Protein: DP02521 (UniProt A5HC98)
Region: residues 950	to 959
Annotation: RNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
Motif F forms part of the fingertips, the flexible loop between fingers strands β20 and β21 that is only fully ordered when the 5′ vRNA is bound (see above).
Upon 5′ vRNA binding (yellow) the backbone interaction with His760 and His761 pulls helix α30 up allowing stabilization of an ordered configuration of the fingertips residues 949–958 (blue sticks).
Cross-references: PDB:5AMQ
Protein: DP02521 (UniProt A5HC98)
Region: residues 950	to 959
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
Motif F forms part of the fingertips, the flexible loop between fingers strands β20 and β21 that is only fully ordered when the 5′ vRNA is bound (see above).
Upon 5′ vRNA binding (yellow) the backbone interaction with His760 and His761 pulls helix α30 up allowing stabilization of an ordered configuration of the fingertips residues 949–958 (blue sticks).
Cross-references: PDB:5AMQ
PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 708	to 717
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows lack of electron densities in this region.
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
Cross-references: PDB:5AMQ
PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 876	to 891
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows lack of electron densities in this region.
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
Cross-references: PDB:5AMQ
PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 1408	to 1424
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A loop (residues 1402 to 1422) at the C-terminal end of the thumb is likely deployed into the polymerase cavity but lacks electron density map, indicating mobility.
The PDB shows the disordered region 1408-1424.
Cross-references: PDB:5AMQ
PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 1532	to 1543
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows lack of electron densities in this region.
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
Cross-references: PDB:5AMQ
PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 950	to 959
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The L1750 model contains 1652 residues (94.4% complete) with several connecting loops missing, some of which become ordered upon 5′ vRNA binding (Figure 1, Data S1).
The PDB shows lack of electron densities in this region.
Cross-references: PDB:5AMR
Protein: DP02521 (UniProt A5HC98)
Region: residues 185	to 270
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The previously described N-terminal endonuclease domain (residues 1–184) (Reguera et al., 2010) is solvent exposed and differently orientated compared to influenza polymerase (Figure 1C, Figure S4A). However, it is clearly flexibly linked to the central polymerase core, as revealed by its lack of density in one 3D class of the EM map (Figure 2B). An extended linker (residues 185–270), analogous to the influenza PA-linker, that packs on and stabilizes the fingers and palm domains of the RdRp (Figure 1B, Figures S4A and S4B), connects the endonuclease to the PA-C like domain (residues 271–759), which is divided into two lobes (Figures 1A and 1B).
Cross-references: EMDB:EMD-2930
Protein: DP02521 (UniProt A5HC98)
Region: residues 185	to 270
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The previously described N-terminal endonuclease domain (residues 1–184) (Reguera et al., 2010) is solvent exposed and differently orientated compared to influenza polymerase (Figure 1C, Figure S4A). However, it is clearly flexibly linked to the central polymerase core, as revealed by its lack of density in one 3D class of the EM map (Figure 2B). An extended linker (residues 185–270), analogous to the influenza PA-linker, that packs on and stabilizes the fingers and palm domains of the RdRp (Figure 1B, Figures S4A and S4B), connects the endonuclease to the PA-C like domain (residues 271–759), which is divided into two lobes (Figures 1A and 1B).
Cross-references: EMDB:EMD-2930
Protein: DP02521 (UniProt A5HC98)
Region: residues 950	to 959
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Upon 5′ vRNA binding (yellow) the backbone interaction with His760 and His761 pulls helix α30 up allowing stabilization of an ordered configuration of the fingertips residues 949–958 (blue sticks).
Cross-references: PDB:5AMQ
Protein: DP02522 (UniProt Q9BE39)
Region: residues 807	to 1935
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
structure corresponding to the converter (701–777) and 1st IQ motif (778–806)
Cross-references: PDB:6FSA
Protein: DP02523 (UniProt Q9UKL0)
Region: residues 1	to 307
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Overall  structure  of  the  human  LSD1/CoREST  in  complex  with  14e.  LSD1  (residues 171-836) is in light blue and CoREST (residues 308-440) in blue.
Cross-references: PDB:2XAS
PDB:2XAJ
PDB:2XAH
PDB:2XAG
PDB:2XAQ
Protein: DP02523 (UniProt Q9UKL0)
Region: residues 441	to 485
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Overall  structure  of  the  human  LSD1/CoREST  in  complex  with  14e.  LSD1  (residues 171-836) is in light blue and CoREST (residues 308-440) in blue.
Cross-references: PDB:2XAS
PDB:2XAJ
PDB:2XAH
PDB:2XAG
PDB:2XAQ
Protein: DP02523 (UniProt Q9UKL0)
Region: residues 1	to 485
Annotation: molecular function regulator (Molecular function)
Evidence: luciferase reporter gene assay evidence used in manual assertion
Supporting statements:
CoREST1 showed the highest transcriptional repression among the three proteins.
Protein: DP02524 (UniProt A5YKK6)
Region: residues 1565	to 1841
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The 3.2-Å-resolution structure of the heterotrimeric complex (Fig. 3, Supplementary Fig. 4c–f and Table 1) contains CNOT1 (1842–2353), CNOT2 (350–540) and CNOT3 (607–748) in a stoichiometry of 1:1:1.
To determine the structure of the CNOT1-C domain, we initially identified a proteolytically stable fragment in CNOT1 (residues 1842–2371; Fig. 1a) that was expressed in a soluble form but failed to crystallize. We then expressed an equivalent fragment of Ct NOT1 (residues 1676–2193; Supplementary Fig. 2), which yielded crystals that diffracted X-rays to 3.2-Å resolution (Table 1).
Cross-references: PDB:4C0D
Protein: DP02524 (UniProt A5YKK6)
Region: residues 1589	to 1607
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Intriguingly, the C-terminal tail of the CN9BD (residues 1,589–1,607) is largely disordered but required for crystallization.
Cross-references: PDB:4CRV
PDB:4CRU
Protein: DP02525 (UniProt P9WGI1)
Region: residues 1	to 224
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we report a cryo-EM structure of Mycobacterium tuberculosis RNAP holoenzyme in complex with Lpm at 3.5-Å resolution.
For the RNAP β' N and C-termini (residues 1-2 and 1282-1316), the central part of the RNAP β' trigger loop (residues 1014-1022), the RNAP β N and C-termini (residues 1-27 and 1145-1172), the RNAP αI N-terminus and C-terminal domain (residues 1-2 and 227-347), the RNAP αII N-terminus and C-terminal domain (residues 1-2 and 233-347), the RNAP ω N-terminus (residues 1-27), σR1.1 (residues 1-224), and a loop and short extended segment of the σR3-σR4 linker (residues 426-433 and 443-445), density was absent, suggesting very high segmental flexibility; these segments were not fitted.
Cross-references: PDB:6FBV
Protein: DP02526 (UniProt C4R4Y0)
Region: residues 1454	to 1743
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 1454-1743 is invisible in the crystal structure of DNA-directed RNA polymerase subunit.
For the type-2 structure, the stalk was manually fitted to the electron density, and then the clashing residues and the regions with missing electron density were deleted from the structure, using Coot
Cross-references: PDB:5X50
PDB:5X51
PDB:5X4Z
Protein: DP02527 (UniProt P04050)
Region: residues 1549	to 1716
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
RNA polymerase II contains a repetitive, intrinsically disordered, C-terminal domain (CTD) composed of heptads of the consensus sequence YSPTSPS. The CTD is heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation and termination, RNA processing and chromatin modification.
Native gel electrophoresis of the S. cerevisae, D. melanogaster and H. sapiens MBP-CTD fusion proteins, with pIs of 5.57, 5.83, 5.93, respectively. Electrophoretic mobility scales with CTD length, suggesting structural homology.
Protein: DP02527 (UniProt P04050)
Region: residues 1456	to 1733
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Intrinsically disordered CTD of RPB1.
Cross-references: PDB:5U5Q
Protein: DP02527 (UniProt P04050)
Region: residues 1446	to 1733
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Intrinsically disordered CTD of RPB1.
Cross-references: PDB:4Y52
Protein: DP02527 (UniProt P04050)
Region: residues 1446	to 1733
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Intrinsically disordered CTD of RPB1.
Cross-references: PDB:3S16
PDB:3S1N
Protein: DP02527 (UniProt P04050)
Region: residues 1455	to 1733
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Intrinsically disordered CTD of RPB1.
Cross-references: PDB:5C4X
Protein: DP02528 (UniProt Q80UG2)
Region: residues 920	to 1229
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In five out of 13 full extracellular structures all ten domains are resolved whereas in the other eight structures some of the C-terminal domains were not modeled due to fragmentary or absent electron density. This indicates that some flexibility is present in the extracellular segment of plexins.
Cross-references: PDB:5L5M
Protein: DP02528 (UniProt Q80UG2)
Region: residues 1004	to 1229
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In five out of 13 full extracellular structures all ten domains are resolved whereas in the other eight structures some of the C-terminal domains were not modeled due to fragmentary or absent electron density. This indicates that some flexibility is present in the extracellular segment of plexins.
Cross-references: PDB:5L5L
Protein: DP02529 (UniProt Q92558)
Region: residues 185	to 494
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For this, we determined the 2.43-Å crystal structure of a complex co-crystallized from a variant of the WIRS-containing peptide (WGAERSM*STFGKEKA, M* for selenomethionine, Fig. 1B) and a minimal inhibited WRC, which lacks the C-terminus of Abi and the proline-rich region of WAVE, miniWRC (Fig. 2, Table S1) (Chen et al., 2010).
Cross-references: PDB:4N78
Protein: DP02529 (UniProt Q92558)
Region: residues 545	to 559
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The A-region of the VCA (residues 545-559) is likely disordered, as it is not observed in the electron density.
Protein: DP02529 (UniProt Q92558)
Region: residues 517	to 526
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure lacks electron density in this region, indication it is disordered. 
Cross-references: PDB:4N78
Protein: DP02529 (UniProt Q92558)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure lacks electron density in this region, indication it is disordered. 
Cross-references: PDB:4N78
Protein: DP02529 (UniProt Q92558)
Region: residues 544	to 559
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure lacks electron density in this region, indication it is disordered. 
Cross-references: PDB:4N78
Protein: DP02530 (UniProt P18564)
Region: residues 492	to 788
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Soluble αVβ6 headpiece was prepared similarly as in ref. 33. In brief, the αV headpiece (residues 1–594) with the M400C mutation was followed by a 3C protease site
Cross-references: PDB:4UM8
PDB:4UM9
Protein: DP02530 (UniProt P18564)
Region: residues 1	to 788
Annotation: molecular function activator activity (Molecular function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
The integrin alpha v beta 6 binds and activates latent TGF beta 1: a mechanism for regulating pulmonary inflammation and fibrosis.
To demonstrate that full-length α vβ 6 also binds to LAP, we repeated affinity chromatography with unlabeled octylglucoside lysates of β 6-transfected SW480 cells (Figure 1D). A 95 kDa protein corresponding to full-length β 6 was detected by Western blotting in eluted fractions from LAP-Sepharose but not from BSA-Sepharose.