3IAY

Ternary complex of DNA polymerase delta

• PDB DOI: https://doi.org/10.2210/pdb3IAY/pdb
• NAKB: 3IAY

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2009-07-15 Released: 2009-09-22 
• Deposition Author(s): Swan, M.K., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta

Swan, M.K., Johnson, R.E., Prakash, L., Prakash, S., Aggarwal, A.K.

(2009) Nat Struct Mol Biol 16: 979-986

• PubMed: 19718023 
• DOI: https://doi.org/10.1038/nsmb.1663
• Primary Citation of Related Structures:  
  3IAY


• PubMed Abstract: 
  

  DNA polymerase delta (Pol delta) is a high-fidelity polymerase that has a central role in replication from yeast to humans. We present the crystal structure of the catalytic subunit of yeast Pol delta in ternary complex with a template primer and an incoming nucleotide. The structure, determined at 2.0-A resolution, catches the enzyme in the act of replication, revealing how the polymerase and exonuclease domains are juxtaposed relative to each other and how a correct nucleotide is selected and incorporated. The structure also reveals the 'sensing' interactions near the primer terminus, which signal a switch from the polymerizing to the editing mode. Taken together, the structure provides a chemical basis for the bulk of DNA synthesis in eukaryotic cells and a framework for understanding the effects of cancer-causing mutations in Pol delta.

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Organizational Affiliation: 

Department of Structural & Chemical Biology, Mount Sinai School of Medicine, New York, New York, USA.

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: 113.83 kDa 
• Atom Count: 8,194 
• Modelled Residue Count: 913 
• Deposited Residue Count: 947 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase delta catalytic subunit	C [auth A]	919	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: Pol3 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P15436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15436  Go to UniProtKB:  P15436

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'	A [auth P]	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'	B [auth T]	16	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	E [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
ACT	J [auth A], K [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth T], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.236 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.077	α = 90
b = 85.948	β = 111.1
c = 86.872	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Swan, M.K., Aggarwal, A.K.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations