2CC3 | pdb_00002cc3

Structure of Agrobacterium tumefaciens VirB8 protein

• PDB DOI: https://doi.org/10.2210/pdb2CC3/pdb

• Classification: SECRETION SYSTEM
• Organism(s): Agrobacterium tumefaciens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-01-11 Released: 2006-01-30 
• Deposition Author(s): Bailey, S., Ward, D., Middleton, R., Grossmann, G., Zambryski, P.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.301 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

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

• PubMed: 16481621 
• DOI: https://doi.org/10.1073/pnas.0511216103
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 33.94 kDa 
• Atom Count: 2,477 
• Modeled Residue Count: 288 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN VIRB8	A, B	150	Agrobacterium tumefaciens	Mutation(s): 0
UniProt
Find proteins for P17798 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore P17798  Go to UniProtKB:  P17798

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.301 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.269	α = 90
b = 72.349	β = 110.66
c = 48.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-30 
Deposition Author(s): Bailey, S., Ward, D., Middleton, R., Grossmann, G., Zambryski, P.C.

Revision History  

• 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