› 6exv

Electron Microscopy
3.6Å resolution

Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin

Released:
DOI: 10.2210/pdb6exv/pdb
PDB entry 6exv coloured by chain, front view.
PDB entry 6exv coloured by chain, side view.
PDB entry 6exv coloured by chain, top view.
Source organisms:
Primary publication:
Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by α-amanitin.
Liu X, Farnung L, Wigge C, Cramer P
J Biol Chem 293 7189-7194 (2018)
PMID: 29550768
Related structures: EMD-3981

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 hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-236761 (preferred)
Entry contents:
13 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (16 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: I3LJR4 (Residues: 1-525, 529-1297, 1304-1968; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1167 amino acids
Theoretical weight: 133.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 134-1300; 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:
Structure 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
Structure domains: Growth Hormone; Chain: A;
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:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (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: Sus scrofa
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: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (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: 14.54 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
Structure domains: Homeodomain-like
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:
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: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
Alpha-amanitin Chain: M
Molecule details ›
Chain: M
Length: 8 amino acids
Theoretical weight: 939 Da
Source organism: Amanita phalloides
UniProt:
  • Canonical: P85421 (Residues: 1-8; Coverage: 35%)
DNA (25-MER) Chain: N
Molecule details ›
Chain: N
Length: 43 nucleotides
Theoretical weight: 13.3 KDa
DNA (36-MER) Chain: T
Molecule details ›
Chain: T
Length: 43 nucleotides
Theoretical weight: 13.18 KDa
RNA (5'-R(P*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3') 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
4 modified residues:
Ligand ILX 1 x ILX
Ligand TRX 1 x TRX
Ligand CSX 1 x CSX
Ligand HYP 1 x HYP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-3981

Quick links

Citations

2 review citations

How to Shut Down Transcription in Archaea during Virus Infection.
Pilotto et al. (2022)
1 more

1 mention without citation

Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by α-amanitin.
Liu et al. (2018)