› 7oop

Electron Microscopy
2.9Å resolution

Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3)

Released:
DOI: 10.2210/pdb7oop/pdb
PDB entry 7oop coloured by chain, front view.
PDB entry 7oop coloured by chain, side view.
PDB entry 7oop coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of human transcription-DNA repair coupling.
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature 598 368-372 (2021)
PMID: 34526721
Related structures: EMD-13010

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 26-mer (preferred)
PDBe Complex ID:
PDB-CPX-236759 (preferred)
Entry contents:
23 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (26 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P11414 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VYD0 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription elongation factor SPT6 Chain: M
Molecule details ›
Chain: M
Length: 1726 amino acids
Theoretical weight: 199.33 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7KZ85 (Residues: 1-1726; Coverage: 100%)
Gene names: KIAA0162, SPT6H, SUPT6H
Sequence domains:
LEO1 helix Chain: R
Molecule details ›
Chain: R
Length: 40 amino acids
Theoretical weight: 3.42 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
RNA polymerase-associated protein CTR9 homolog Chain: S
Molecule details ›
Chain: S
Length: 1173 amino acids
Theoretical weight: 133.72 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6PD62 (Residues: 1-1173; Coverage: 100%)
Gene names: CTR9, KIAA0155, SH2BP1
Sequence domains:
RNA polymerase-associated protein LEO1 Chain: U
Molecule details ›
Chain: U
Length: 666 amino acids
Theoretical weight: 75.51 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WVC0 (Residues: 1-666; Coverage: 100%)
Gene names: LEO1, RDL
Sequence domains: Leo1-like protein
RNA polymerase II-associated factor 1 homolog Chain: V
Molecule details ›
Chain: V
Length: 531 amino acids
Theoretical weight: 60.05 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N7H5 (Residues: 1-531; Coverage: 100%)
Gene names: PAF1, PD2
Sequence domains: Paf1
Superkiller complex protein 8 Chain: Y
Molecule details ›
Chain: Y
Length: 305 amino acids
Theoretical weight: 33.62 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9GZS3 (Residues: 1-305; Coverage: 100%)
Gene names: SKIC8, WDR61
Sequence domains: WD domain, G-beta repeat
Parafibromin Chain: Z
Molecule details ›
Chain: Z
Length: 531 amino acids
Theoretical weight: 60.67 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6P1J9 (Residues: 1-531; Coverage: 100%)
Gene names: C1orf28, CDC73, HRPT2
Sequence domains:
DNA excision repair protein ERCC-8 Chain: a
Molecule details ›
Chain: a
Length: 396 amino acids
Theoretical weight: 44.11 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13216 (Residues: 1-396; Coverage: 100%)
Gene names: CKN1, CSA, ERCC8
Sequence domains: WD domain, G-beta repeat
DNA excision repair protein ERCC-6 Chain: b
Molecule details ›
Chain: b
Length: 1493 amino acids
Theoretical weight: 168.7 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q03468 (Residues: 1-1493; Coverage: 100%)
Gene names: CSB, ERCC6
Sequence domains:
UV-stimulated scaffold protein A Chain: c
Molecule details ›
Chain: c
Length: 709 amino acids
Theoretical weight: 80.72 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q2YD98 (Residues: 1-709; Coverage: 100%)
Gene names: KIAA1530, UVSSA
Sequence domains:
DNA damage-binding protein 1 Chain: d
Molecule details ›
Chain: d
Length: 1140 amino acids
Theoretical weight: 127.1 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
NTS Chain: N
Molecule details ›
Chain: N
Length: 47 nucleotides
Theoretical weight: 14.49 KDa
TS Chain: T
Molecule details ›
Chain: T
Length: 47 nucleotides
Theoretical weight: 14.27 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 45 nucleotides
Theoretical weight: 14.49 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-13010
Expression system: Trichoplusia ni

Quick links

Citations

10 review citations

Nucleotide excision repair: a versatile and smart toolkit.
Zhang et al. (2022)
9 more

1 mention without citation

Structure of the transcribing RNA polymerase II-Elongin complex.
Chen et al. (2023)