› 6bm4

X-ray diffraction
2.95Å resolution

Pol II elongation complex with an abasic lesion at i-1 position,soaking UMPNPP

Released:
DOI: 10.2210/pdb6bm4/pdb
Model geometry
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PDB entry 6bm4 coloured by chain, front view.
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Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Wang W, Walmacq C, Chong J, Kashlev M, Wang D
Proc Natl Acad Sci U S A 115 E2538-E2545 (2018)
PMID: 29487211

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-119612 (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
Expression system: 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 S288C
Expression system: 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 (5'-D(P*CP*AP*(3DR)P*CP*TP*CP*TP*TP*GP*AP*TP*G)-3') Chain: T
RNA (5'-R(*AP*UP*CP*AP*AP*GP*AP*GP*A)-3') Chain: R

Ligands and Environments

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

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: C2
Unit cell:
a: 168.72Å b: 220.43Å c: 193.15Å
α: 90° β: 100.97° γ: 90°
R-values:
R R work R free
0.236 0.234 0.26
Expression system: Saccharomyces cerevisiae

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Citations

9 review citations

DNA Damage and Associated DNA Repair Defects in Disease and Premature Aging.
Tiwari et al. (2019)
8 more

3 mentions without citation

Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair.
Wang et al. (2018)
2 more

PDB-REDO

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