2YGC | pdb_00002ygc

Structure of vaccinia virus D13 scaffolding protein

• PDB DOI: https://doi.org/10.2210/pdb2YGC/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Vaccinia virus Western Reserve
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-04-13 Released: 2011-07-20 
• Deposition Author(s): Bahar, M.W., Graham, S.C., Stuart, D.I., Grimes, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Insights Into the Evolution of a Complex Virus from the Crystal Structure of Vaccinia Virus D13.

Bahar, M.W., Graham, S.C., Stuart, D.I., Grimes, J.M.

(2011) Structure 19: 1011

• PubMed: 21742267 
• DOI: https://doi.org/10.1016/j.str.2011.03.023
• Primary Citation of Related Structures:  
  2YGB, 2YGC


• PubMed Abstract: 
  

  The morphogenesis of poxviruses such as vaccinia virus (VACV) sees the virion shape mature from spherical to brick-shaped. Trimeric capsomers of the VACV D13 protein form a transitory, stabilizing lattice on the surface of the initial spherical immature virus particle. The crystal structure of D13 reveals that this major scaffolding protein comprises a double β barrel "jelly-roll" subunit arranged as pseudo-hexagonal trimers. These structural features are characteristic of the major capsid proteins of a lineage of large icosahedral double-stranded DNA viruses including human adenovirus and the bacteriophages PRD1 and PM2. Structure-based phylogenetic analysis confirms that VACV belongs to this lineage, suggesting that (analogously to higher organism embryogenesis) early poxvirus morphogenesis reflects their evolution from a lineage of viruses sharing a common icosahedral ancestor.

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Organizational Affiliation: 
• The Division of Structural Biology and the Oxford Protein Production Facility, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 192.98 kDa 
• Atom Count: 12,992 
• Modeled Residue Count: 1,626 
• Deposited Residue Count: 1,707 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIFAMPICIN RESISTANCE PROTEIN	A, B, C	569	Vaccinia virus Western Reserve	Mutation(s): 1
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve)) Explore P68440  Go to UniProtKB:  P68440

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.58	α = 90
b = 190.58	β = 90
c = 252.96	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Bahar, M.W., Graham, S.C., Stuart, D.I., Grimes, J.M.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary