3SAM | pdb_00003sam

Structure of D13, the scaffolding protein of vaccinia virus (mutant D513G)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 
    0.201 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Membrane remodeling by the double-barrel scaffolding protein of poxvirus.

Hyun, J.K.Accurso, C.Hijnen, M.Schult, P.Pettikiriarachchi, A.Mitra, A.K.Coulibaly, F.

(2011) PLoS Pathog 7: e1002239-e1002239

  • DOI: https://doi.org/10.1371/journal.ppat.1002239
  • Primary Citation Related Structures: 
    3SAM, 3SAQ

  • PubMed Abstract: 

    In contrast to most enveloped viruses, poxviruses produce infectious particles that do not acquire their internal lipid membrane by budding through cellular compartments. Instead, poxvirus immature particles are generated from atypical crescent-shaped precursors whose architecture and composition remain contentious. Here we describe the 2.6 Å crystal structure of vaccinia virus D13, a key structural component of the outer scaffold of viral crescents. D13 folds into two jellyrolls decorated by a head domain of novel fold. It assembles into trimers that are homologous to the double-barrel capsid proteins of adenovirus and lipid-containing icosahedral viruses. We show that, when tethered onto artificial membranes, D13 forms a honeycomb lattice and assembly products structurally similar to the viral crescents and immature particles. The architecture of the D13 honeycomb lattice and the lipid-remodeling abilities of D13 support a model of assembly that exhibits similarities with the giant mimivirus. Overall, these findings establish that the first committed step of poxvirus morphogenesis utilizes an ancestral lipid-remodeling strategy common to icosahedral DNA viruses infecting all kingdoms of life. Furthermore, D13 is the target of rifampicin and its structure will aid the development of poxvirus assembly inhibitors.


  • Organizational Affiliation
    • School of Biological Sciences, the University of Auckland, Auckland, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 195.3 kDa 
  • Atom Count: 13,528 
  • Modeled Residue Count: 1,627 
  • Deposited Residue Count: 1,728 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rifampicin resistance protein
A, B, C
576Vaccinia virus WRMutation(s): 1 
Gene Names: D13D13LVACWR118
UniProt
Find proteins for P68440 (Vaccinia virus (strain Western Reserve))
Explore P68440 
Go to UniProtKB:  P68440
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68440
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free:  0.201 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.63α = 90
b = 189.63β = 90
c = 255.13γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-19
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations