3I4M

8-oxoguanine containing RNA polymerase II elongation complex D

• PDB DOI: https://doi.org/10.2210/pdb3I4M/pdb
• NAKB: 3I4M

• Classification: TRANSCRIPTION,TRANSFERASE/DNA-RNA HYBRID
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2009-07-02 Released: 2009-09-08 
• Deposition Author(s): Damsma, G.E., Cramer, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.230 (DCC) 

Starting Model: experimental

Literature

Molecular basis of transcriptional mutagenesis at 8-oxoguanine

Damsma, G.E., Cramer, P.

(2009) J Biol Chem 284: 31658-31663

• PubMed: 19758983 
• DOI: https://doi.org/10.1074/jbc.M109.022764
• Primary Citation of 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A1B1C1D1E1F1G1H1I1J1K1L1 

Biological assembly 1 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050  Go to UniProtKB:  P04050

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518  Go to UniProtKB:  P08518

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	324	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370  Go to UniProtKB:  P16370

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433  Go to UniProtKB:  P20433

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434  Go to UniProtKB:  P20434

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435  Go to UniProtKB:  P20435

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087  Go to UniProtKB:  P34087

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436  Go to UniProtKB:  P20436

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999  Go to UniProtKB:  P27999

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139  Go to UniProtKB:  P22139

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902  Go to UniProtKB:  P38902

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422  Go to UniProtKB:  P40422

Entity ID: 13
Molecule	Chains	Length	Organism	Image
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]	26	N/A

Entity ID: 14
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3')	N	12	N/A

Entity ID: 15
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*CP*AP*UP*C*UP*UP*CP*CP*AP*GP*GP*CP*CP*U)-3')	O [auth P]	16	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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	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), 0.250 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.230 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 220.646	α = 90
b = 392.003	β = 90
c = 281.455	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-08 
Deposition Author(s): Damsma, G.E., Cramer, P.

Revision History  

• 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