LiteFold/DisProt huggingface dataset:
Protein: DP02477 (UniProt Q01970)
Region: residues 471	to 572
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 471–572 correspond to a region of the X-Y linker that has low sequence homology and is typically poorly ordered
separates a triose phosphate isomerase (TIM) barrel-like catalytic domain into X and Y halves
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 471	to 572
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 471–572 correspond to a region of the X-Y linker that has low sequence homology and is typically poorly ordered
separates a triose phosphate isomerase (TIM) barrel-like catalytic domain into X and Y halves
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 883	to 933
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The CTD linker (residues 883–933) is not observed in the structure
The CTD Linker Is Required for Gαq Activation
Because the sequence of the CTD linker is not conserved among PLCβ isozymes, its length and/or flexibility seems to be required for the proximal and distal CTDs to make all the interactions necessary for activation by Gαq.
Furthermore, deletion of the CTD linker leads to complete loss of Gαq activation in our assays
PLCβ also has a ~400 amino acid C-terminal extension to the catalytic core that contains the proximal and distal C-terminal domains (CTDs) separated by a non-conserved, low complexity linker of variable length
The distal (purple) and proximal CTDs are connected by the disordered CTD linker
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 883	to 933
Annotation: molecular function activator activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The CTD linker (residues 883–933) is not observed in the structure
The CTD Linker Is Required for Gαq Activation
Because the sequence of the CTD linker is not conserved among PLCβ isozymes, its length and/or flexibility seems to be required for the proximal and distal CTDs to make all the interactions necessary for activation by Gαq.
Furthermore, deletion of the CTD linker leads to complete loss of Gαq activation in our assays
PLCβ also has a ~400 amino acid C-terminal extension to the catalytic core that contains the proximal and distal C-terminal domains (CTDs) separated by a non-conserved, low complexity linker of variable length
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 882	to 1234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was observed for residues 11–470 and 573–881 in chain A of PLCβ3, and 10–196, 199–470, and 575–881 in the second.
The CTD linker (residues 883–933) is not observed in the structure
In the distal CTD, the Dα3-Dα4 (residues 1009–1025) and Dα4-Dα5 (residues 1108–1114) loops and C-terminal residues 1193–1234 lacked electron density, consistent with being disordered (Supplementary Fig. 3a).
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 934	to 1192
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To elucidate a structural basis for the functional roles of the distal CTD, we used X-ray crystallography and single particle electron cryo-microscopy (cryo EM) to determine the structure of human full-length PLCβ3 in complex with activated Gαq, revealing the distal CTD in the context of a fully functional signaling complex where it forms unanticipated interactions with Gαq and the catalytic core of PLCβ that likely contribute to regulation.
The distal CTD (residues 934–1192) consists of three primarily anti-parallel helical segments that extend nearly the full-length (~140 Å) of the domain (Fig. 1b, ​,2a).2a). The first segment contains the Dα1 (residues 935–946), Dα2 (954–958) and Dα3 (960–1008) helices. Dα3 forms an extended anti-parallel coiled-coil interaction with the Dα4 helix (residues 1027–1107) in the second segment. Dα4 in turn forms an extended anti-parallel coiled-coil interaction with Dα5 (residues 1115–1183) in the third segment. The Dα1 and Dα2 helices at the beginning of the first segment, and Dα6 (residues 1184–1192) at the end of the third segment, form “arms” that cross the same face of the domain and pack against the principal helices of the other two segments
Cross-references: PDB:4GNK
Protein: DP02477 (UniProt Q01970)
Region: residues 934	to 1192
Annotation: molecular adaptor activity (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
To elucidate a structural basis for the functional roles of the distal CTD, we used X-ray crystallography and single particle electron cryo-microscopy (cryo EM) to determine the structure of human full-length PLCβ3 in complex with activated Gαq, revealing the distal CTD in the context of a fully functional signaling complex where it forms unanticipated interactions with Gαq and the catalytic core of PLCβ that likely contribute to regulation.
The distal CTD (residues 934–1192) consists of three primarily anti-parallel helical segments that extend nearly the full-length (~140 Å) of the domain (Fig. 1b, ​,2a).2a). The first segment contains the Dα1 (residues 935–946), Dα2 (954–958) and Dα3 (960–1008) helices. Dα3 forms an extended anti-parallel coiled-coil interaction with the Dα4 helix (residues 1027–1107) in the second segment. Dα4 in turn forms an extended anti-parallel coiled-coil interaction with Dα5 (residues 1115–1183) in the third segment. The Dα1 and Dα2 helices at the beginning of the first segment, and Dα6 (residues 1184–1192) at the end of the third segment, form “arms” that cross the same face of the domain and pack against the principal helices of the other two segments
Protein: DP02478 (UniProt Q6SJQ7)
Region: residues 132	to 330
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In this study, we determined the X-ray crystal structure of the soluble CD300lf (sCD300lf) and the murine norovirus capsid protruding domain complex at a 2.05-Å resolution. 
Region adjacent to the crystallized domain sCD300lf characterized by missing electron density.
Cross-references: PDB:5OR7
Protein: DP02479 (UniProt O60502)
Region: residues 11	to 58
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
OGA-L consists of an N-terminal catalytic domain (GH84), a helical domain, extensive regions predicted as disordered, and a C-terminal domain of unknown function having similarity to histone acetyl transferase (HAT) domains
residues 11-58, 341-370, 535-536, 596-598, 674-675 and 696-706 are disordered
Authors termed “Split1” their construct of OGA comprising amino acids 11-396 (N-terminal fragment) and 535-715 (C-terminal fragment) that yielded crystals suitable for structure determination.
Cross-references: PDB:5M7U
PDB:5M7T
PDB:5M7S
PDB:5M7R
Protein: DP02479 (UniProt O60502)
Region: residues 341	to 370
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
OGA-L consists of an N-terminal catalytic domain (GH84), a helical domain, extensive regions predicted as disordered, and a C-terminal domain of unknown function having similarity to histone acetyl transferase (HAT) domains
residues 11-58, 341-370, 535-536, 596-598, 674-675 and 696-706 are disordered
Authors termed “Split1” their construct of OGA comprising amino acids 11-396 (N-terminal fragment) and 535-715 (C-terminal fragment) that yielded crystals suitable for structure determination.
Cross-references: PDB:5M7U
PDB:5M7T
PDB:5M7S
PDB:5M7R
Protein: DP02479 (UniProt O60502)
Region: residues 696	to 706
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
OGA-L consists of an N-terminal catalytic domain (GH84), a helical domain, extensive regions predicted as disordered, and a C-terminal domain of unknown function having similarity to histone acetyl transferase (HAT) domains
residues 11-58, 341-370, 535-536, 596-598, 674-675 and 696-706 are disordered
Authors termed “Split1” their construct of OGA comprising amino acids 11-396 (N-terminal fragment) and 535-715 (C-terminal fragment) that yielded crystals suitable for structure determination.
Cross-references: PDB:5M7U
PDB:5M7T
PDB:5M7S
PDB:5M7R
Protein: DP02479 (UniProt O60502)
Region: residues 11	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues that were still disordered in monomers A and B were Gly11–Gly56, Ser348–Glu369, Lys535 and Pro707–Tyr715 for monomer B only.
Cross-references: PDB:6HKI
Protein: DP02479 (UniProt O60502)
Region: residues 348	to 369
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues that were still disordered in monomers A and B were Gly11–Gly56, Ser348–Glu369, Lys535 and Pro707–Tyr715 for monomer B only.
Cross-references: PDB:6HKI
Protein: DP02479 (UniProt O60502)
Region: residues 341	to 371
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The (β/α)8 barrel includes amino acids 58–340, whereas 341–371 are disordered.
Protein: DP02480 (UniProt Q12102)
Region: residues 423	to 625
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we report the crystal structures of human CPSF-73 at 2.1 Å resolution, complexed with zinc ions and a sulfate that may mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1p) at 2.5 Å resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-β-lactamase domain and a novel β-CASP domain. 
There are, however, significant differences in the structures of CPSF-100 and CPSF-73 (Supplemental Fig. 4). Most importantly, motifs for zinc binding in the metallo-β-lactamase domain are missing in CPSF-100 (Supplemental Fig. 2b), and therefore this protein cannot bind zinc and is unlikely to possess nuclease activity. In addition, the β-CASP domain of CPSF-100 (Fig. 2b) is much larger than that of CPSF-73, but contains a highly flexible segment (Supplemental Results and Supplemental Fig. 5).
Several segments of CPSF-73 are disordered in these crystals (1-6, 113-121, 289-299 in the
presence, and 1-8, 113-121, 184-188, 272-304 in the absence of zinc), as is the case in the
structure of yeast CPSF-100 (269-275, 389-396, 423-625).
Cross-references: PDB:2I7X
Protein: DP02481 (UniProt P46674)
Region: residues 1	to 142
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
residues 1–142 showed little potential for forming secondary structure.
Cross-references: PDB:5L3T
Protein: DP02481 (UniProt P46674)
Region: residues 551	to 1301
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We could not find additional density consistent with residues beyond 551 (connecting the Sac3 M-subcomplex and the Sac3 CID-subcomplex) and so it is likely that this linker is flexible, consistent with the random orientation observed for the CID region relative to the M-region in negatively stained electron micrographs.
No other difference density was observed that could correspond to the CID domain of the complex (containing Sac3 residues 727–805, together with two Sus1 chains and a Cdc31 chain), consistent with the crystals containing only the N-terminal half of Sac3 (up to about residue 555) together with Thp1 and Sem1.
and the CID-subcomplex, consisting of Sac3 residues ∼720–805 bound to Cdc31 and two Sus1 chains and which, in Saccharomyces cerevisiae, binds to the nuclear pore complex (NPC) to tether the complex close to the nuclear basket to facilitate localization of genes such as GAL1
Cross-references: PDB:5L3T
Protein: DP02481 (UniProt P46674)
Region: residues 720	to 805
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
and the CID-subcomplex, consisting of Sac3 residues ∼720–805 bound to Cdc31 and two Sus1 chains and which, in Saccharomyces cerevisiae, binds to the nuclear pore complex (NPC) to tether the complex close to the nuclear basket to facilitate localization of genes such as GAL1
Cross-references: PDB:5L3T
PDB:5G5P
Protein: DP02481 (UniProt P46674)
Region: residues 720	to 805
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
and the CID-subcomplex, consisting of Sac3 residues ∼720–805 bound to Cdc31 and two Sus1 chains and which, in Saccharomyces cerevisiae, binds to the nuclear pore complex (NPC) to tether the complex close to the nuclear basket to facilitate localization of genes such as GAL1
Cross-references: PDB:5L3T
PDB:5G5P
Protein: DP02481 (UniProt P46674)
Region: residues 551	to 719
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We could not find additional density consistent with residues beyond 551 (connecting the Sac3 M-subcomplex and the Sac3 CID-subcomplex) and so it is likely that this linker is flexible, consistent with the random orientation observed for the CID region relative to the M-region in negatively stained electron micrographs.
Cross-references: PDB:5L3T
PDB:5G5P
Protein: DP02481 (UniProt P46674)
Region: residues 720	to 805
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There was however, no clear additional density that could be identified with the linkers between these helices or with the CID region of the complex, consistent with the CID region not having a defined orientation relative to the M-region as observed in the negatively-stained material. It is likely that within the cryo-EM micrographs recorded that the CID-subcomplex is also present in random orientations, however since the CID-subcomplex is effectively little more than a single α-helix with small proteins attached, the signal-to-noise is too poor for the particles to be detected with confidence
The structure of the TREX-2 M-region determined by cryo-EM has been deposited in the Electron Microscopy Data Bank (accession No. EMD-3440)
Cross-references: PDB:5G5P
Protein: DP02481 (UniProt P46674)
Region: residues 720	to 805
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CID-subcomplex, consisting of Sac3 residues ∼720–805 bound to Cdc31 and two Sus1 chains and which, in Saccharomyces cerevisiae, binds to the nuclear pore complex (NPC) to tether the complex close to the nuclear basket to facilitate localization of genes such as GAL1
Cross-references: PDB:5G5P
PDB:5L3T
Protein: DP02483 (UniProt Q8ZRP0)
Region: residues 1	to 426
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The  crystal  structure  was  determined  by molecular replacement to a resolution of 2.92 Å. Only the BamA barrel domain was found in the structure, indicating that the BamAB complex may be  too flexible to be crystallized,  while  the  BamA  POTRA  domains  and  BamB may  be  cleaved  by contaminant   proteases   during   the   protein   crystallization.
There is one BamA molecule per asymmetric unit. The BamA barrel is formed by 16 β-strands with residues Asn427-Gly801.
Cross-references: PDB:5OR1
Protein: DP02484 (UniProt P0AD27)
Region: residues 1	to 244
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Region 1-244 is not visible in the crystal structure of E. coli YejM
Cross-references: PDB:5I5H
Protein: DP02485 (UniProt P40709)
Region: residues 1	to 244
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All the proteins were purified, and the PbgA245-586 from S. typhimurium Str. LT2 (StPbgA245-586) and E. coli (EcPbgA245-586) were crystallized
The crystals of StPbgA191-586 belong to the space group P21 with cell dimensions a = 41.49 Å, b = 196.39 Å, c = 45.66 Å, α = γ = 90° and β = 107.53°. The StPbgA191-586 structure was determined by molecular replacement to 2.19 Å resolution; residues 191–245 has no visible electron density so were either disordered or cleaved.
Cross-references: PDB:5I5D
PDB:5I5F
Protein: DP02487 (UniProt P22473)
Region: residues 1	to 288
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The atomic structure of RDV was determined at 3.5 A resolution by X-ray crystallography. 
The present model contains two P3 subunits (P3A, residues 50–1016; P3B, residues 1–1019), 13 P8 subunits (PA, residues 1–47 and 55–421; PB, residues 1–48 and 55–421; PC, residues 1–49 and 54–421; QA, residues 1–421; QB, residues 1–421; QC, residues 1–47 and 54–421; RA, residues 1–421; RB, residues 1–48 and 53–421; RC, residues 1–421; SA, residues 1–421; SB, residues 1–50 and 53–421; SC, residues 1–47 and 56–421; T, residues 1–421), and a fragment of P7 (residues 289–300).
We present here the atomic structure of RDV, determined at 3.5 Å resolution by X-ray crystallography. The model consists of P3 inner capsid proteins, P8 outer capsid proteins, and fragments of P7, the nucleic acid binding protein. The atomic structure suggests a self-assembly mechanism for both homologous and heterologous capsid proteins.
Cross-references: PDB:1UF2
Protein: DP02487 (UniProt P22473)
Region: residues 301	to 506
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The atomic structure of RDV was determined at 3.5 A resolution by X-ray crystallography.
The present model contains two P3 subunits (P3A, residues 50–1016; P3B, residues 1–1019), 13 P8 subunits (PA, residues 1–47 and 55–421; PB, residues 1–48 and 55–421; PC, residues 1–49 and 54–421; QA, residues 1–421; QB, residues 1–421; QC, residues 1–47 and 54–421; RA, residues 1–421; RB, residues 1–48 and 53–421; RC, residues 1–421; SA, residues 1–421; SB, residues 1–50 and 53–421; SC, residues 1–47 and 56–421; T, residues 1–421), and a fragment of P7 (residues 289–300).
We present here the atomic structure of RDV, determined at 3.5 Å resolution by X-ray crystallography. The model consists of P3 inner capsid proteins, P8 outer capsid proteins, and fragments of P7, the nucleic acid binding protein. The atomic structure suggests a self-assembly mechanism for both homologous and heterologous capsid proteins.
Cross-references: PDB:1UF2
Protein: DP02487 (UniProt P22473)
Region: residues 289	to 300
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The electron density map clearly shows side chain features, and it allowed us to identify the segment as a fragment of P7 protein (Figure 1D). P7 protein is thought to be a nonspecific nucleic acid binding protein (Ueda et al., 1997
). This fragment of P7 protein binds tightly to part of P3 protein with a β sheet structure (Figure 1D). This tight interaction between the core and the nucleic acid binding protein P7 might be important for the transport of nucleic acids into viral particles during the process of viral assembly.
Cross-references: PDB:1UF2
Protein: DP02487 (UniProt P22473)
Region: residues 289	to 300
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The electron density map clearly shows side chain features, and it allowed us to identify the segment as a fragment of P7 protein (Figure 1D). P7 protein is thought to be a nonspecific nucleic acid binding protein (Ueda et al., 1997
). This fragment of P7 protein binds tightly to part of P3 protein with a β sheet structure (Figure 1D). This tight interaction between the core and the nucleic acid binding protein P7 might be important for the transport of nucleic acids into viral particles during the process of viral assembly.
Cross-references: PDB:1UF2
Protein: DP02487 (UniProt P22473)
Region: residues 289	to 300
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The electron density map clearly shows side chain features, and it allowed us to identify the segment as a fragment of P7 protein (Figure 1D). P7 protein is thought to be a nonspecific nucleic acid binding protein (Ueda et al., 1997). This fragment of P7 protein binds tightly to part of P3 protein with a β sheet structure (Figure 1D). This tight interaction between the core and the nucleic acid binding protein P7 might be important for the transport of nucleic acids into viral particles during the process of viral assembly.
Cross-references: PDB:1UF2
Protein: DP02488 (UniProt O28769)
Region: residues 1	to 233
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model comprises four chains of the fragment N234 to K338.
When tracing the density it became obvious that there were actually 4 chains in the asymmetric unit, corresponding to the C-terminal fragment spanning residues N234 to K338.
Cross-references: PDB:4CQ4
Protein: DP02489 (UniProt Q9YIJ1)
Region: residues 1	to 208
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There was no ordered electron density observed for residues 1 to 208.
The first 208 amino acids of the VP, comprising the VP1 unique region with a phospholipase A2 domain, the VP1/VP2 common region (residues 137 to 192), and the first 15 residues of VP3, are not observed.
Cross-references: PDB:3NTT
Protein: DP02490 (UniProt D1A4G7)
Region: residues 200	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the full protein is present in the crystal (Figure S3C), the N-terminal “DUF” domain and linker1 are disordered in the structure and could not be modeled
Cross-references: PDB:4NH0
PDB:4N1A