› 8ebx

Electron Microscopy
3.6Å resolution

XPA repositioning Core7 of TFIIH relative to XPC-DNA lesion (AP)

Released:
DOI: 10.2210/pdb8ebx/pdb
PDB entry 8ebx coloured by chain, front view.
PDB entry 8ebx coloured by chain, side view.
PDB entry 8ebx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Kim J, Li CL, Chen X, Cui Y, Golebiowski FM, Wang H, Hanaoka F, Sugasawa K, Yang W
Nature (2023)
PMID: 37076618
Related structures: EMD-28001

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-230654 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (12 distinct):
General transcription and DNA repair factor IIH helicase/translocase subunit XPB Chain: A
Molecule details ›
Chain: A
Length: 782 amino acids
Theoretical weight: 89.4 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P19447 (Residues: 1-782; Coverage: 100%)
Gene names: ERCC3, XPB, XPBC
Sequence domains:
General transcription and DNA repair factor IIH helicase subunit XPD Chain: B
Molecule details ›
Chain: B
Length: 768 amino acids
Theoretical weight: 88.02 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P18074 (Residues: 1-760; Coverage: 100%)
Gene names: ERCC2, XPD, XPDC
Sequence domains:
General transcription factor IIH subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 548 amino acids
Theoretical weight: 62.12 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P32780 (Residues: 1-548; Coverage: 100%)
Gene names: BTF2, GTF2H1
Sequence domains:
General transcription factor IIH subunit 4 Chain: D
Molecule details ›
Chain: D
Length: 462 amino acids
Theoretical weight: 52.25 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92759 (Residues: 1-462; Coverage: 100%)
Gene name: GTF2H4
Sequence domains:
General transcription factor IIH subunit 2 Chain: E
Molecule details ›
Chain: E
Length: 417 amino acids
Theoretical weight: 46.93 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13888 (Residues: 1-395; Coverage: 100%)
Gene names: BTF2P44, GTF2H2
Sequence domains:
General transcription factor IIH subunit 3 Chain: F
Molecule details ›
Chain: F
Length: 308 amino acids
Theoretical weight: 34.42 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13889 (Residues: 1-308; Coverage: 100%)
Gene name: GTF2H3
Sequence domains: Transcription factor Tfb4
General transcription factor IIH subunit 5 Chain: G
Molecule details ›
Chain: G
Length: 71 amino acids
Theoretical weight: 8.06 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q6ZYL4 (Residues: 1-71; Coverage: 100%)
Gene names: C6orf175, GTF2H5, TTDA
Sequence domains: Transcription factor TFIIH complex subunit Tfb5
DNA repair protein complementing XP-C cells Chain: H
Molecule details ›
Chain: H
Length: 950 amino acids
Theoretical weight: 107.44 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q01831 (Residues: 1-940; Coverage: 100%)
Gene names: XPC, XPCC
Sequence domains:
Centrin-2 Chain: J
Molecule details ›
Chain: J
Length: 172 amino acids
Theoretical weight: 19.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P41208 (Residues: 1-172; Coverage: 100%)
Gene names: CALT, CEN2, CETN2
Sequence domains: EF-hand domain pair
DNA repair protein complementing XP-A cells Chain: K
Molecule details ›
Chain: K
Length: 273 amino acids
Theoretical weight: 31.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P23025 (Residues: 1-273; Coverage: 100%)
Gene names: XPA, XPAC
Sequence domains:
DNA (Ap) Chain: L
Molecule details ›
Chain: L
Length: 40 nucleotides
Theoretical weight: 12.18 KDa
DNA Chain: M
Molecule details ›
Chain: M
Length: 40 nucleotides
Theoretical weight: 12.18 KDa

Ligands and Environments

3 bound ligands:
Ligand SF4 1 x SF4
Ligand ZN 6 x ZN
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-28001
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

1 review citation

UV-DDB as a General Sensor of DNA Damage in Chromatin: Multifaceted Approaches to Assess Its Direct Role in Base Excision Repair.
Raja et al. (2023)
2 other articles

1 mention without citation

Lesion recognition by XPC, TFIIH and XPA in DNA excision repair.
Kim et al. (2023)