Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.96 kDa 
• Atom Count: 5,437 
• Modelled Residue Count: 540 
• Deposited Residue Count: 544 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 3OHA

Yeast DNA polymerase eta inserting dCTP opposite an 8oxoG lesion

• PDB DOI: 10.2210/pdb3OHA/pdb
• NDB: NA0698

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-17 Released: 2010-12-22 
• Deposition Author(s): Silverstein, T.D., Jain, R., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Literature

Structural basis for error-free replication of oxidatively damaged DNA by yeast DNA polymerase eta.

Silverstein, T.D., Jain, R., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2010) Structure 18: 1463-1470

• PubMed: 21070945 
• DOI: 10.1016/j.str.2010.08.019
• Primary Citation of Related Structures:  
  3OHA, 3OHB


• PubMed Abstract: 
  

7,8-dihydro-8-oxoguanine (8-oxoG) adducts are formed frequently by the attack of oxygen-free radicals on DNA. They are among the most mutagenic lesions in cells because of their dual coding potential, where, in addition to normal base-pairing of 8-oxoG(anti) with dCTP, 8-oxoG in the syn conformation can base pair with dATP, causing G to T transversions. We provide here for the first time a structural basis for the error-free replication of 8-oxoG lesions by yeast DNA polymerase η (Polη). We show that the open active site cleft of Polη can accommodate an 8-oxoG lesion in the anti conformation with only minimal changes to the polymerase and the bound DNA: at both the insertion and post-insertion steps of lesion bypass. Importantly, the active site geometry remains the same as in the undamaged complex and provides a basis for the ability of Polη to prevent the mutagenic replication of 8-oxoG lesions in cells.

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Organizational Affiliation: 

Department of Structural & Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase eta	A	520	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: DBH1, RAD30, YDR419W EC: 2.7.7.7
UniProt
Find proteins for Q04049 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04049  Go to UniProtKB:  Q04049

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*CP*TP*CP*CP*CP*CP*TP*(DOC))-3'	B [auth P]	11	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(P*TP*(8OG)P*GP*AP*GP*GP*GP*GP*AP*GP*GP*AP*C)-3'	C [auth T]	13	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	D [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
SO4	E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.195 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.039	α = 90
b = 227.635	β = 90
c = 86.077	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-22 
Deposition Author(s): Silverstein, T.D., Jain, R., Aggarwal, A.K.

Revision History  

• Version 1.0: 2010-12-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description