› 8oev

Electron Microscopy
2.86Å resolution

Structure of the mammalian Pol II-SPT6-Elongin complex, lacking ELOA latch (composite structure, structure 3)

Released:
DOI: 10.2210/pdb8oev/pdb
PDB entry 8oev coloured by chain, front view.
PDB entry 8oev coloured by chain, side view.
PDB entry 8oev coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the transcribing RNA polymerase II-Elongin complex.
Chen Y, Kokic G, Dienemann C, Dybkov O, Urlaub H, Cramer P
OpenAccess logo Nat Struct Mol Biol (2023)
PMID: 37932450
Related structures: EMD-16837

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-240658 (preferred)
Entry contents:
16 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (19 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1251 amino acids
Theoretical weight: 142.43 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 50-1300; Coverage: 96%)
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: 184 amino acids
Theoretical weight: 20.96 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 1-184; Coverage: 100%)
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 subunit Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
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: A0A8W4F9W9 (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: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase II, I and III subunit K 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
Elongin-A Chain: M
Molecule details ›
Chain: M
Length: 801 amino acids
Theoretical weight: 90.36 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q14241 (Residues: 1-772; Coverage: 100%)
  • Best match: Q14241-1 (Residues: 1-798)
Gene names: ELOA, MSTP059, TCEB3
Sequence domains:
Elongin-C Chain: O
Molecule details ›
Chain: O
Length: 112 amino acids
Theoretical weight: 12.49 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15369 (Residues: 1-112; Coverage: 100%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
Elongin-B Chain: Q
Molecule details ›
Chain: Q
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Transcription elongation factor SPT6 Chain: S
Molecule details ›
Chain: S
Length: 1729 amino acids
Theoretical weight: 199.6 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7KZ85 (Residues: 1-1726; Coverage: 100%)
Gene names: KIAA0162, SPT6H, SUPT6H
Sequence domains:
Non-Template DNA Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 46 nucleotides
Theoretical weight: 14.84 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.86Å
Relevant EMDB volumes: EMD-16837
Expression system: Trichoplusia ni

Quick links

Citations

1 mention without citation

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