3I4M: 8-oxoguanine Containing RNA Polymerase II Elongation Complex D

Citation:
Abstract
Structure-function analysis has revealed the mechanism of yeast RNA polymerase II transcription at 8-oxoguanine (8-oxoG), the major DNA lesion resulting from oxidative stress. When polymerase II encounters 8-oxoG in the DNA template strand, it can misincorporate adenine, which forms a Hoogsteen bp with 8-oxoG at the active center. This requires rotation of the 8-oxoG base from the standard anti- to an uncommon syn-conformation, which likely occurs during 8-oxoG loading into the active site. The misincorporated adenine escapes intrinsic proofreading, resulting in transcriptional mutagenesis that is observed directly by mass spectrometric RNA analysis.
PDB ID: 3I4MDownload
MMDB ID: 76597
PDB Deposition Date: 2009/7/2
Updated in MMDB: 2009/09 
Experimental Method:
x-ray diffraction
Resolution: 3.7  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 3I4M: pentadecameric; determined by author
Molecular Components in 3I4M
Label Count Molecule
Proteins (12 molecules)
1
DNA-directed RNA Polymerase II Subunit Rpb1
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb2
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb3
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb4
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc1
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc2
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb7
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc3
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb9
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc5
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb11
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc4
Molecule annotation
Nucleotides(3 molecules)
1
DNA (5'-d(*ap*g*cp*tp*cp*ap*ap*gp*tp*ap*cp*tp*tp*ap*(8og) P*gp*cp*cp*(bru)p*gp*gp*tp*cp*ap*tp*t)-3')
Molecule annotation
1
DNA (5'-d(*ap*gp*tp*ap*cp*tp*tp*gp*ap*gp*cp*t)-3')
Molecule annotation
1
RNA (5'-r(*up*gp*cp*ap*up*c*up*up*cp*cp*ap*gp*gp*cp*cp*u)- 3')
Molecule annotation
Chemicals (9 molecules)
1
1
2
8
* Click molecule labels to explore molecular sequence information.

Citing MMDB
.