9RC4 | pdb_00009rc4

Crystal structure of VirJ domain 1 from Brucella

• PDB DOI: https://doi.org/10.2210/pdb9RC4/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella abortus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-27 Released: 2025-09-03 
• Deposition Author(s): Dugelay, C., Ferrarin, S., Terradot, L.
• Funding Organization(s): Centre National de la Recherche Scientifique (CNRS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of the virulence protein J (VirJ) domain 1 from Brucella abortus.

Dugelay, C., Ferrarin, S., Terradot, L.

(2025) Acta Crystallogr F Struct Biol Commun 81: 374-380

• PubMed: 40824293 
• DOI: https://doi.org/10.1107/S2053230X25006697
• Primary Citation of Related Structures:  
  9RC4


• PubMed Abstract: 
  

  Virulence protein J (VirJ) is a periplasmic protein encoded by the bacterial pathogen Brucella abortus and is important for its virulence. The VirJ homologue AcvB from Agrobacterium tumefaciens was found to be a lysyl-phosphatidylglycerol hydrolase that contains two domains, D1 and D2. Interestingly, both VirJ and AcvB are associated with the type IV secretion system (T4SS) activity in the respective bacteria. To date, no structural information is available for these proteins, limiting our understanding of their function. Here, we have purified, crystallized and determined the crystal structure of the N-terminal domain 1 of VirJ (VirJ ^D1 ) at a resolution of 1.7 Å. Our structural analysis shows that VirJ ^D1 adopts an α/β-hydrolase fold but lacks the characteristic catalytic triad. The structure presented here may help to decipher the function of VirJ in Brucella spp. and other bacterial pathogens, as well as its contribution to the T4SS function.

---

Organizational Affiliation: 
• Institut de Biologie et Chimie des Protéines, UMR 5086 Molecular Microbiology and Structural Biochemistry, CNRS-Université Lyon 1, 7 Passage du Vercors, 69007 Lyon, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.45 kDa 
• Atom Count: 3,453 
• Modeled Residue Count: 436 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virulence factor family protein	A, B	229	Brucella abortus	Mutation(s): 0  Gene Names: NBW10_01030, NBW10_16820
UniProt
Find proteins for A0A0F6AUT4 (Brucella abortus (strain S19)) Explore A0A0F6AUT4  Go to UniProtKB:  A0A0F6AUT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.638	α = 80.921
b = 47.235	β = 89.057
c = 54.124	γ = 86.135

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Dugelay, C., Ferrarin, S., Terradot, L.

---

Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references