PDBe 3j0k

Electron Microscopy
36Å resolution

Orientation of RNA polymerase II within the human VP16-Mediator-pol II-TFIIF assembly

Released:
Source organism: Homo sapiens
Related structures: EMD-5343

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 12-mer (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1455 amino acids
Theoretical weight: 163.18 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P04050 (Residues: 1-1455)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P08518 (Residues: 1-1224)
Gene names: RPB150, RPB2, RPO22, YOR151C
DNA-directed RNA polymerase II subunit RPB3 Chain: C
Molecule details ›
Chain: C
Length: 268 amino acids
Theoretical weight: 30.14 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P16370 (Residues: 1-268)
Gene names: RPB3, YIL021W
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P20433 (Residues: 1-221)
Gene names: J0654, RPB4, YJL140W
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P20434 (Residues: 1-215)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 84 amino acids
Theoretical weight: 9.68 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P20435 (Residues: 72-155)
Gene names: P9677.8, RPB6, RPO26, YPR187W
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P34087 (Residues: 1-171)
Gene names: D9509.22, RPB7, YDR404C
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P20436 (Residues: 1-146)
Gene names: RPB8, YOR224C, YOR50-14
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P27999 (Residues: 1-122)
Gene names: RPB9, YGL070C
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P22139 (Residues: 1-70)
Gene names: RPB10, YOR210W
DNA-directed RNA polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Homo sapiens
UniProt:
  • Best match: P38902 (Residues: 1-120)
Gene names: RPB11, YOL005C
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide Chain: L
Molecule details ›
Chain: L
Length: 46 amino acids
Theoretical weight: 5.25 KDa
Source organism: Homo sapiens

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 36Å
Relevant EMDB volumes: EMD-5343