6WJV | pdb_00006wjv

Structure of the Saccharomyces cerevisiae polymerase epsilon holoenzyme

• PDB DOI: https://doi.org/10.2210/pdb6WJV/pdb
• EM Map EMD-21701: EMDB EMDataResource

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2020-04-14 Released: 2020-07-08 
• Deposition Author(s): Yuan, Z., Georgescu, R., Schauer, G.D., O'Donnell, M., Li, H.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the polymerase epsilon holoenzyme and atomic model of the leading strand replisome.

Yuan, Z., Georgescu, R., Schauer, G.D., O'Donnell, M.E., Li, H.

(2020) Nat Commun 11: 3156

• DOI: https://doi.org/10.1038/s41467-020-16910-5

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 379.21 kDa 
• Atom Count: 19,593 
• Modeled Residue Count: 2,567 
• Deposited Residue Count: 3,308 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase epsilon catalytic subunit A	A	2,222	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: POL2, DUN2, YNL262W, N0825 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21951  Go to UniProtKB:  P21951

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase epsilon subunit B	B [auth 2]	689	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DPB2, YPR175W, P9705.7
UniProt
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P24482  Go to UniProtKB:  P24482

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase epsilon subunit C	C [auth 3]	201	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DPB3, YBR278W, YBR2015
UniProt
Find proteins for P27344 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27344  Go to UniProtKB:  P27344

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase epsilon subunit D	D [auth 4]	196	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: DPB4, YDR121W
UniProt
Find proteins for Q04603 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04603  Go to UniProtKB:  Q04603

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Yuan, Z., Georgescu, R., Schauer, G.D., O'Donnell, M., Li, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM131754
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM115809
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary