6P1H

Cryo-EM Structure of DNA Polymerase Delta Holoenzyme

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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


Literature

Cryo-EM structure and dynamics of eukaryotic DNA polymerase delta holoenzyme.

Jain, R., Rice, W.J., Malik, R., Johnson, R.E., Prakash, L., Prakash, S., Ubarretxena-Belandia, I., Aggarwal, A.K.

(2019) Nat Struct Mol Biol 26: 955-962

  • DOI: https://doi.org/10.1038/s41594-019-0305-z
  • Primary Citation of Related Structures:  
    6P1H

  • PubMed Abstract: 

    • DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits ...

    DNA polymerase δ (Polδ) plays pivotal roles in eukaryotic DNA replication and repair. Polδ is conserved from yeast to humans, and mutations in human Polδ have been implicated in various cancers. Saccharomyces cerevisiae Polδ consists of catalytic Pol3 and the regulatory Pol31 and Pol32 subunits. Here, we present the near atomic resolution (3.2 Å) cryo-EM structure of yeast Polδ holoenzyme in the act of DNA synthesis. The structure reveals an unexpected arrangement in which the regulatory subunits (Pol31 and Pol32) lie next to the exonuclease domain of Pol3 but do not engage the DNA. The Pol3 C-terminal domain contains a 4Fe-4S cluster and emerges as the keystone of Polδ assembly. We also show that the catalytic and regulatory subunits rotate relative to each other and that this is an intrinsic feature of the Polδ architecture. Collectively, the structure provides a framework for understanding DNA transactions at the replication fork.

    Organizational Affiliation: 

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. aneel.aggarwal@mssm.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta catalytic subunit1,119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POL3, CDC2, TEX1, YDL102W, D2366
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P15436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P15436
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UniProt GroupP15436
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta small subunit494Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POL31, HUS2, HYS2, SDP5, YJR006W, J1427, YJR83.7
EC: 2.7.7.7
UniProt
Find proteins for P46957 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P46957
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UniProt GroupP46957
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POL32, YJR043C, J1626
UniProt
Find proteins for P47110 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47110 
Go to UniProtKB:  P47110
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UniProt GroupP47110
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (30-MER)D [auth P],
E [auth T]		30synthetic construct
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Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other