Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 118404.65 
• Atom Count: 8259 
• Residue Count: 1010 
• Unique protein chains: 1

5N2E

Structure of the E9 DNA polymerase from vaccinia virus

• DOI: 10.2210/pdb5N2E/pdb

• Classification: TRANSFERASE
• Organism(s): Vaccinia virus (strain Copenhagen)
• Expression System: Trichoplusia ni


• Deposited: 2017-02-07 Released: 2017-11-29 
• Deposition Author(s): Tarbouriech, N., Burmeister, W.P., Iseni, F.
• Funding Organization(s): French National Research Agency 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 

Literature

The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding.

Tarbouriech, N., Ducournau, C., Hutin, S., Mas, P.J., Man, P., Forest, E., Hart, D.J., Peyrefitte, C.N., Burmeister, W.P., Iseni, F.

(2017) Nat Commun 8: 1455-1455

• PubMed: 29129932 
• DOI: 10.1038/s41467-017-01542-z
• Primary Citation of Related Structures:  
  5N2H, 5N2G


• PubMed Abstract: 
  

Vaccinia virus (VACV), the prototype member of the Poxviridae, replicates in the cytoplasm of an infected cell. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Here we present the crystal structure of full-length E9 at 2.7 Å resolution that permits identification of important poxvirus-specific structural insertions. One insertion in the palm domain interacts with C-terminal residues of A20 and thus serves as the processivity factor-binding site. This is in strong contrast to all other family B polymerases that bind their co-factors at the C terminus of the thumb domain. The VACV E9 structure also permits rationalization of polymerase inhibitor resistance mutations when compared with the closely related eukaryotic polymerase delta-DNA complex.

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Organizational Affiliation: 

Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase	A	1010	Vaccinia virus (strain Copenhagen)	Mutation(s): 0  Gene Names: POL EC: 2.7.7.7
Find proteins for P20509 (Vaccinia virus (strain Copenhagen)) Go to UniProtKB:  P20509

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	A	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DTT	A	2,3-DIHYDROXY-1,4-DITHIOBUTANE 1,4-DITHIOTHREITOL C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
MES	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.236 
• R-Value Work: 0.186 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 133.415	α = 90.00
b = 133.415	β = 90.00
c = 230.525	γ = 120.00

Software Package:

Software Name	Purpose
Aimless	data scaling
SOLVE	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-07 
• Released Date: 2017-11-29 
• Deposition Author(s): Tarbouriech, N., Burmeister, W.P., Iseni, F.

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Funding Organization	Location	Grant Number
French National Research Agency	France	13-BSV8-0014

Revision History 

• Version 1.0: 2017-11-29
  Type: Initial release
• Version 1.1: 2018-10-17
  Type: Data collection, Source and taxonomy, Structure summary