› 2r7z

X-ray diffraction
3.8Å resolution

Cisplatin lesion containing RNA polymerase II elongation complex

Released:
DOI: 10.2210/pdb2r7z/pdb
Model geometry
Fit model/data
PDB entry 2r7z coloured by chain, front view.
PDB entry 2r7z coloured by chain, side view.
PDB entry 2r7z coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Mechanism of transcriptional stalling at cisplatin-damaged DNA.
Damsma GE, Alt A, Brueckner F, Carell T, Cramer P
Nat Struct Mol Biol 14 1127-33 (2007)
PMID: 17994106

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

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115823 (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:
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 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(*TP*AP*CP*TP*TP*GUP*CP*CP*CP*TP*CP*CP*TP*CP*AP*T)-3' Chain: T
5'-D(*CP*AP*AP*GP*TP*AP*G)-3' Chain: N
5'-R(*UP*UP*UP*GP*AP*GP*GP*AP*GP*G)-3' Chain: P

Ligands and Environments

3 bound ligands:
Ligand CPT 1 x CPT
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: SLS BEAMLINE X06SA
Spacegroup: C2221
Unit cell:
a: 222.062Å b: 393.123Å c: 283.733Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.215 0.215 0.24

Quick links

Citations

30 review citations

Transcription-coupled DNA repair: two decades of progress and surprises.
Hanawalt et al. (2008)
29 more

6 mentions without citation

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