2CC3

Structure of Agrobacterium tumefaciens VirB8 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Agrobacterium Tumefaciens Virb8 Structure Reveals Potential Protein-Protein Interactions Sites.

Bailey, S.Ward, D.Middleton, R.Grossmann, J.G.Zambryski, P.C.

(2006) Proc Natl Acad Sci U S A 103: 2582

  • DOI: https://doi.org/10.1073/pnas.0511216103
  • Primary Citation of Related Structures:  
    2CC3

  • PubMed Abstract: 

    Bacterial type IV secretion systems (T4SS) translocate DNA and/or proteins to recipient cells, thus providing a mechanism for conjugative transfer of genetic material and bacterial pathogenesis. Here we describe the first structure of a core component from the archetypal Agrobacterium tumefaciens T4SS: the 2.2-A resolution crystal structure of the VirB8 periplasmic domain (pVirB8(AT)). VirB8 forms a dimer in the crystal, and we identify residues likely important for stabilization of the dimer interface. Structural comparison of pVirB8(AT) with Brucella suis VirB8 confirms that the monomers have a similar fold. In addition, the pVirB8(AT) dimer superimposes very closely on the B. suis VirB8 dimer, supporting the proposal that dimer formation in the crystal reflects self-interactions that are biologically significant. The evolutionary conservation level for each residue was obtained from a data set of 84 VirB8 homologs and projected onto the protein structure to indicate conserved surface patches that likely contact other T4SS proteins.


  • Organizational Affiliation

    Molecular Biophysics Group, Council for the Central Laboratory of the Research Councils Daresbury Laboratory, Warrington WA4 4AD, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN VIRB8
A, B
150Agrobacterium tumefaciensMutation(s): 0 
UniProt
Find proteins for P17798 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P17798 
Go to UniProtKB:  P17798
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17798
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.269α = 90
b = 72.349β = 110.66
c = 48.844γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description