› 3hox

X-ray diffraction
3.65Å resolution

Complete RNA polymerase II elongation complex V

Released:
DOI: 10.2210/pdb3hox/pdb
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PDB entry 3hox coloured by chain, front view.
PDB entry 3hox coloured by chain, side view.
PDB entry 3hox coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P
Mol Cell 34 710-21 (2009)
PMID: 19560423

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 pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-116369 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (15 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:
Structure domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
DNA-directed RNA polymerase II subunit RPB4 Chain: D
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 polymerase II subunit RPB7 Chain: G
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
5'-D(*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' Chain: N
5'-D(*AP*GP*CP*TP*C*AP*AP*GP*TP*AP*GP*TP*TP*AP*AP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3' Chain: T
5'-R(*UP*GP*CP*AP*UP*UP*U*CP*AP*AP*CP*CP*AP*GP*GP*CP*UP*U)-3' Chain: P

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
1 modified residue:
Ligand BRU 1 x BRU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 221.617Å b: 393.716Å c: 282.576Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.212 0.25

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Citations

24 review citations

Transcript Elongation by RNA Polymerase II.
Selth et al. (2010)
23 more

4 mentions without citation

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

PDB-REDO

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