Virulence-associated protein VapB from the intracellular pathogen Rhodococcus equi

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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Conformational changes of loops highlight a potential binding site in Rhodococcus equi VapB.

Geerds, C.Haas, A.Niemann, H.H.

(2021) Acta Crystallogr F Struct Biol Commun 77: 246-253

  • DOI: https://doi.org/10.1107/S2053230X2100738X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.

  • Organizational Affiliation

    Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virulence associated protein VapB
A, B
113Prescottella equiMutation(s): 0 
Gene Names: pVAPB_vapB
Membrane Entity: Yes 
Find proteins for B4F366 (Rhodococcus hoagii)
Explore B4F366 
Go to UniProtKB:  B4F366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4F366
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.94α = 90
b = 65.34β = 90
c = 124.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-09-01
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description