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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.236 (Depositor), 0.220 (DCC)
R-Value Work:
0.193 (Depositor), 0.180 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15436
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(APTPCPCPTPCPCPCPCPTPAP(DOC))-3'	A [auth P]	12	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(TPAPAPGPGPTPAPGPGPGPGPAPGPGPAPT)-3'	B [auth T]	16	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DCP Query on DCP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₃ P₃ RGWHQCVHVJXOKC-SHYZEUOFSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth T] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth T] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain D [auth T] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	D [auth T], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth T] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth T] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.236 (Depositor), 0.220 (DCC)
R-Value Work: 0.193 (Depositor), 0.180 (DCC)
R-Value Observed: 0.195 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Swan, M.K.

Aggarwal, A.K.

Revision History (Full details and data files)

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