› 3s2h

X-ray diffraction
3.3Å resolution

RNA Polymerase II Initiation Complex with a 6-nt RNA containing a 2[prime]-iodo ATP

Released:
DOI: 10.2210/pdb3s2h/pdb
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Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Initiation complex structure and promoter proofreading.
Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD
Science 333 633-7 (2011)
PMID: 21798951

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 dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116859 (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 S288C
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 S288C
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
DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3') Chain: T
RNA (5'-R(*AP*GP*AP*GP*GP*(2IA))-3') Chain: R

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
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: 165.533Å b: 221.608Å c: 194.056Å
α: 90° β: 99.67° γ: 90°
R-values:
R R work R free
0.193 0.19 0.24

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Citations

7 review citations

Control of transcriptional elongation.
Kwak et al. (2013)
6 more

2 mentions without citation

Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.
Kaplan CD. (2013)
1 more

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