9JDH | pdb_00009jdh

Crystal structure of the T6SS effector BtaeB-NTD from Bacteroides fragilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A conserved adaptor orchestrates co-secretion of synergistic type VI effectors in gut Bacteroidota.

Li, W.Zheng, S.Xu, X.He, J.Jiao, X.Wang, M.Hu, W.Li, S.Jiang, X.Lim, B.Shao, F.Gao, X.

(2025) Cell Host Microbe 33: 1901

  • DOI: https://doi.org/10.1016/j.chom.2025.09.012
  • Primary Citation of Related Structures:  
    9JDH, 9JDI, 9JG8

  • PubMed Abstract: 

    Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are released via structural proteins such as VgrG, but the secretion timing and coordination are unclear. Here, we report two effectors, BtpeA (Bacteroides T6SS phosphatase effector A) and BtaeB (Bacteroides T6SS amidase effector B), within the Bacteroidota T6SS that exert distinct cell-wall destructive activities critical for interspecies competition but whose secretion is interdependent. BtpeA and BtaeB co-secretion requires an adaptor protein, BtapC (Bacteroides T6SS adaptor protein C), that mediates the sequential assembly of the pre-firing complex, VgrG-BtpeA-BtaeB-BtapC. Structural analyses of this quaternary complex elucidate multi-cargo loading mechanisms with a conserved loop in BtaeB serving as a "checkpoint" to ensure BtpeA co-secretion. During mouse colonization, the combined activities of BtpeA and BtaeB significantly exceed the sum of the individual effectors. These findings unveil a T6SS-mediated co-delivery mechanism that ensures functional synergism of effectors, highlighting potential applications in modulating gut microbiota.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase C39-like domain-containing protein390Bacteroides fragilisMutation(s): 0 
Gene Names: FSA06_12440
UniProt
Find proteins for A0AB38PQQ6 (Bacteroides fragilis)
Explore A0AB38PQQ6 
Go to UniProtKB:  A0AB38PQQ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AB38PQQ6
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.67α = 90
b = 49.37β = 90
c = 183.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China323B2003

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references
  • Version 1.2: 2025-11-26
    Changes: Database references