9UX0 | pdb_00009ux0

Crystal structure of the virulence effector VepA in complex with its secretion chaperone VecA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of effector recognition by the T3SS chaperone VecA from Vibrio parahaemolyticus.

Iimori, M.Oki, H.Akeda, Y.Ishii, E.Kodama, T.Ueda, T.Nakamura, S.Matsuda, S.Kawahara, K.Iida, T.

(2025) Biochem Biophys Res Commun 776: 152190-152190

  • DOI: https://doi.org/10.1016/j.bbrc.2025.152190
  • Primary Citation of Related Structures:  
    9UWZ, 9UX0

  • PubMed Abstract: 

    Many pathogenic gram-negative bacteria utilise the type III secretion system (T3SS), a specific protein injection apparatus, to translocate virulence effectors into host cells, modulating host cell functions and establishing infection. To facilitate the precise cytosolic transport of effectors to T3SS, a class of proteins called chaperones plays a crucial role. However, a limited number of available structural data on chaperone-effector complexes hampers understanding of the mechanisms underlying this process. In Vibrio parahaemolyticus, a major causative agent of seafood-associated acute gastroenteritis in humans, T3SS chaperone VecA transports its cognate membrane-disrupting effector, VepA. Here, we determined the crystal structure of VecA alone and in complex with VepA at resolutions of 2.20 Å and 2.49 Å, respectively. While the overall protein fold and the hydrophobic cleft that accommodates an N-terminal β-motif of effectors were conserved among T3SS chaperones, the structural analysis revealed that surface residues are remarkably different, reflecting their substrate specificity. Additionally, unlike other reported structures of the T3SS chaperone-effector complexes, in which the effectors are partially unfolded and wrapped around the chaperone, VepA adopts a highly folded conformation in the complex. This compact structure appears to protect the fragile glycine-rich transmembrane domain of VepA and suggests that upon secretion, VepA undergoes conformational changes, including α-helix formation, allowing the transmembrane domain to embed into and disrupt the membrane of organelles containing its binding target, V-ATPase. These findings elucidate the chaperone-mediated regulation of effector transport and function of the bacterial virulence-related T3SS.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Osaka, Suita, Osaka, 565-0871, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cation transporter493Vibrio parahaemolyticusMutation(s): 0 
Gene Names: VP1680
UniProt
Find proteins for Q87P38 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87P38 
Go to UniProtKB:  Q87P38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87P38
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CesT family type III secretion system chaperone
B, C
157Vibrio parahaemolyticusMutation(s): 0 
Gene Names: VP1682
UniProt
Find proteins for Q87P37 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87P37 
Go to UniProtKB:  Q87P37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87P37
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.241 (Depositor), 0.241 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.848α = 90
b = 152.934β = 90
c = 101.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP24KJ1623

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references