› 6drd

Electron Microscopy
3.9Å resolution

RNA Pol II(G)

Released:
DOI: 10.2210/pdb6drd/pdb
PDB entry 6drd coloured by chain, front view.
PDB entry 6drd coloured by chain, side view.
PDB entry 6drd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1.
Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, Chait BT, Asturias FJ, Roeder RG
Nat Struct Mol Biol 25 859-867 (2018)
PMID: 30190596
Related structures: EMD-7997

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 tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127501 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 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: Homo sapiens
UniProt:
  • Canonical: P24928 (Residues: 1-1970; Coverage: 100%)
Gene names: POLR2, POLR2A
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.07 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P30876 (Residues: 1-1174; Coverage: 100%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 31.48 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19387 (Residues: 1-275; Coverage: 100%)
Gene names: A-152E5.7, POLR2C
Sequence domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O15514 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.66 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P19388 (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: 14.49 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61218 (Residues: 1-127; Coverage: 100%)
Gene names: POLR2F, POLRF
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: Homo sapiens
UniProt:
  • Canonical: P62487 (Residues: 1-172; Coverage: 100%)
Gene names: POLR2G, RPB7
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: Homo sapiens
UniProt:
  • Canonical: P52434 (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: Homo sapiens
UniProt:
  • Canonical: P36954 (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: Homo sapiens
UniProt:
  • Canonical: P62875 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase II subunit RPB11-a Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P52435 (Residues: 1-117; Coverage: 100%)
Gene names: POLR2J, POLR2J1
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: Homo sapiens
UniProt:
  • Canonical: P53803 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
DNA-directed RNA polymerase II subunit GRINL1A Chain: M
Molecule details ›
Chain: M
Length: 62 amino acids
Theoretical weight: 5.76 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P0CAP2 (Residues: 300-316; Coverage: 5%)
Gene names: GRINL1A, POLR2M

Ligands and Environments

1 bound ligand:
Ligand ZN 5 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-7997

Quick links

Citations

5 review citations

MicroRNA-139, an Emerging Gate-Keeper in Various Types of Cancer.
Stavast et al. (2022)
4 more

1 mention without citation

ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia.
Lao et al. (2022)