› 5flm

Electron Microscopy
3.4Å resolution

Structure of transcribing mammalian RNA polymerase II

Released:
DOI: 10.2210/pdb5flm/pdb
PDB entry 5flm coloured by chain, front view.
PDB entry 5flm coloured by chain, side view.
PDB entry 5flm coloured by chain, top view.
Source organism: Bos taurus
Primary publication:
Structure of transcribing mammalian RNA polymerase II.
Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P
Nature 529 551-4 (2016)
PMID: 26789250
Related structures: EMD-3218

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 pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107716 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (15 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.44 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: G3MZY8 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: A5PJW8 (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: 31.47 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q3T0Q3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.35 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q1JQ91 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q2T9T3 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
Structure 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: Bos taurus
UniProt:
  • Canonical: Q32PE0 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q5E9B8 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence domains:
Structure 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: Bos taurus
UniProt:
  • Canonical: F2Z4H3 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.51 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q32P73 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
Structure domains: N-terminal domain of TfIIb
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: Bos taurus
UniProt:
  • Canonical: Q32P78 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Bos taurus
UniProt:
  • Canonical: Q32P79 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
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: Bos taurus
UniProt:
  • Canonical: Q3ZBC0 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
DNA, DNA-RNA ELONGATION SCAFFOLD Chain: N
Molecule details ›
Chain: N
Length: 39 nucleotides
Theoretical weight: 12.09 KDa
DNA, DNA-RNA ELONGATION SCAFFOLD Chain: T
Molecule details ›
Chain: T
Length: 39 nucleotides
Theoretical weight: 11.94 KDa
RNA, DNA-RNA ELONGATION SCAFFOLD Chain: P
Molecule details ›
Chain: P
Length: 20 nucleotides
Theoretical weight: 6.41 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: 3.4Å
Relevant EMDB volumes: EMD-3218

Quick links

Citations

24 review citations

Unravelling biological macromolecules with cryo-electron microscopy.
Fernandez-Leiro et al. (2016)
23 more

27 mentions without citation

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
26 more