› 1r9s

X-ray diffraction
4.25Å resolution

RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MATCHED NUCLEOTIDE

Released:
DOI: 10.2210/pdb1r9s/pdb
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PDB entry 1r9s coloured by chain, front view.
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PDB entry 1r9s coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
Westover KD, Bushnell DA, Kornberg RD
Cell 119 481-9 (2004)
PMID: 15537538

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114505 (preferred)
Entry contents:
10 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (12 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:
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:
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
DNA strand Chain: T
RNA strand Chain: R

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand UTP 1 x UTP
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2
Unit cell:
a: 169.647Å b: 222.338Å c: 194.316Å
α: 90° β: 101.67° γ: 90°
R-values:
R R work R free
0.367 0.349 0.398

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Citations

42 review citations

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
Yang et al. (2006)
41 more

9 mentions without citation

Structural perspective on mutations affecting the function of multisubunit RNA polymerases.
Trinh et al. (2006)
8 more

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