› 2nvy

X-ray diffraction
3.4Å resolution

RNA Polymerase II form II in 150 mM Mn+2

Released:
DOI: 10.2210/pdb2nvy/pdb
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PDB entry 2nvy coloured by chain, front view.
PDB entry 2nvy coloured by chain, side view.
PDB entry 2nvy coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD
Cell 127 941-54 (2006)
PMID: 17129781

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero decamer (preferred)
hetero icosamer
Assembly name:
PDBe Complex ID:
PDB-CPX-137354 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 1-1733; Coverage: 100%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Gene names: RPB150, RPB2, RPO22, YOR151C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
DNA-directed RNA polymerase II subunit RPB9 Chain: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
DNA-directed RNA polymerase II subunit RPB11 Chain: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I222
Unit cell:
a: 118.036Å b: 218.914Å c: 369.549Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.251 0.249 0.323

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Citations

59 review citations

Looping back to leap forward: transcription enters a new era.
Levine et al. (2014)
58 more

1 mention without citation

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
Wang et al. (2006)

PDB-REDO

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