5N2G | pdb_00005n2g

Structure of the E9 DNA polymerase from vaccinia virus in complex with manganese


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.227 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.183 (Depositor) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

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

  • DOI: https://doi.org/10.1038/s41467-017-01542-z
  • Primary Citation Related Structures: 
    5N2E, 5N2G, 5N2H

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 118.7 kDa 
  • Atom Count: 8,470 
  • Modeled Residue Count: 999 
  • Deposited Residue Count: 1,009 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase1,009Vaccinia virus CopenhagenMutation(s): 0 
Gene Names: POLE9L
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
Find proteins for P20509 (Vaccinia virus (strain Copenhagen))
Explore P20509 
Go to UniProtKB:  P20509
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20509
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
L [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
DTT

Query on DTT



Download:Ideal Coordinates CCD File
K [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
H [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.227 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.183 (Depositor) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.007α = 90
b = 134.007β = 90
c = 230.189γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-13-BSV8-0014

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary