› 2ja7

X-ray diffraction
3.8Å resolution

CPD lesion containing RNA Polymerase II elongation complex C

Released:
DOI: 10.2210/pdb2ja7/pdb
PDB entry 2ja7 coloured by chain, front view.
PDB entry 2ja7 coloured by chain, side view.
PDB entry 2ja7 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
CPD damage recognition by transcribing RNA polymerase II.
Brueckner F, Hennecke U, Carell T, Cramer P
Science 315 859-62 (2007)
PMID: 17290000

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-115422 (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 Chains: A, M
Molecule details ›
Chains: A, M
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 Chains: B, N
Molecule details ›
Chains: B, N
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 Chains: C, O
Molecule details ›
Chains: C, O
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB4 Chains: D, P
Molecule details ›
Chains: D, P
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chains: F, R
Molecule details ›
Chains: F, R
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase II subunit RPB7 Chains: G, S
Molecule details ›
Chains: G, S
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chains: H, T
Molecule details ›
Chains: H, T
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase II subunit RPB9 Chains: I, U
Molecule details ›
Chains: I, U
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
Structure domains: N-terminal domain of TfIIb
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chains: J, V
Molecule details ›
Chains: J, V
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase II subunit RPB11 Chains: K, W
Molecule details ›
Chains: K, W
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chains: L, X
Molecule details ›
Chains: L, X
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3' Chains: 1, 4
Molecule details ›
Chains: 1, 4
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TP*TTP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' Chains: 2, 5
Molecule details ›
Chains: 2, 5
Length: 25 nucleotides
Theoretical weight: 7.93 KDa
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3' Chains: 3, 6
Molecule details ›
Chains: 3, 6
Length: 11 nucleotides
Theoretical weight: 3.51 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ZN 16 x ZN
1 modified residue:
Ligand BRU 2 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 394.358Å b: 221.862Å c: 283.105Å
α: 90° β: 90.56° γ: 90°
R-values:
R R work R free
0.257 0.257 0.275

Quick links

Citations

41 review citations

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

5 mentions without citation

XPB and XPD helicases in TFIIH orchestrate DNA duplex opening and damage verification to coordinate repair with transcription and cell cycle via CAK kinase.
Fuss et al. (2011)
4 more