4QCB

Protein-DNA complex of Vaccinia virus D4 with double-stranded non-specific DNA

• PDB DOI: https://doi.org/10.2210/pdb4QCB/pdb
• NAKB: 4QCB

• Classification: HYDROLASE/DNA
• Organism(s): Vaccinia virus WR
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-05-09 Released: 2015-06-10 
• Deposition Author(s): Schormann, N., Banerjee, S., Ricciardi, R., Chattopadhyay, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.265 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase.

Schormann, N., Banerjee, S., Ricciardi, R., Chattopadhyay, D.

(2015) BMC Struct Biol 15: 10-10

• PubMed: 26031450 
• DOI: https://doi.org/10.1186/s12900-015-0037-1
• Primary Citation of Related Structures:  
  4QCB


• PubMed Abstract: 
  

  Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized.

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Organizational Affiliation: 

Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.42 kDa 
• Atom Count: 4,019 
• Modelled Residue Count: 448 
• Deposited Residue Count: 466 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A, B	221	Vaccinia virus WR	Mutation(s): 2  Gene Names: VACWR109, D4R, UNG EC: 3.2.2.27
UniProt
Find proteins for P04303 (Vaccinia virus (strain Western Reserve)) Explore P04303  Go to UniProtKB:  P04303

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*AP*AP*AP*CP*GP*TP*TP*TP*GP*C)-3'	C, D	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.265 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.389	α = 90
b = 92.327	β = 90
c = 142.859	γ = 90

Software Package:

Software Name	Purpose
RAPD	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-10 
Deposition Author(s): Schormann, N., Banerjee, S., Ricciardi, R., Chattopadhyay, D.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Source and taxonomy
• Version 1.2: 2018-04-18
  Changes: Data collection, Database references
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description