3I4M | pdb_00003i4m

8-oxoguanine containing RNA polymerase II elongation complex D

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 
    0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.227 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Molecular basis of transcriptional mutagenesis at 8-oxoguanine

Damsma, G.E., Cramer, P.

(2009) J Biological Chem 284: 31658-31663

  • DOI: https://doi.org/10.1074/jbc.M109.022764
  • Primary Citation Related Structures: 
    3I4M, 3I4N

  • PubMed 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.

    • Organizational Affiliation: 
    • Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Macromolecule Content 

  • Total Structure Weight: 532.28 kDa 
  • Atom Count: 32,355 
  • Modeled Residue Count: 4,007 
  • Deposited Residue Count: 4,625 
  • Unique protein chains: 12
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupP04050
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP08518
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3324Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP20433
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP20434
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP20435
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP34087
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP20436
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP27999
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38902
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP40422
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Reference Sequence
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Entity ID: 13
MoleculeChains LengthOrganismImage
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')M [auth T]26N/A
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3')12N/A
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Reference Sequence
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Entity ID: 15
MoleculeChains LengthOrganismImage
RNA (5'-R(*UP*GP*CP*AP*UP*C*UP*UP*CP*CP*AP*GP*GP*CP*CP*U)-3')O [auth P]16N/A
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN

Query on ZN


Download:Ideal Coordinates CCD File
Q [auth A]
R [auth A]
S [auth B]
T [auth C]
U [auth I]
Q [auth A],
R [auth A],
S [auth B],
T [auth C],
U [auth I],
V [auth I],
W [auth J],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
P [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free:  0.258 (Depositor), 0.253 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.646α = 90
b = 392.003β = 90
c = 281.455γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-01-16
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary