9UU2 | pdb_00009uu2

Outer membrane protein OmpA-c-like domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A nonenzymatic effector disrupts Bacteroides cell wall homeostasis via OmpA targeting to mediate interbacterial competition.

He, J.Chen, Z.Jiang, K.Yang, Y.Li, W.Wang, X.Xu, X.Zheng, S.Jiao, X.Chen, X.Huo, L.Lim, B.Liu, S.J.Gao, X.

(2025) Proc Natl Acad Sci U S A 122

  • DOI: https://doi.org/10.1073/pnas.2513207122
  • Primary Citation of Related Structures:  
    9UU0, 9UU1, 9UU2

  • PubMed Abstract: 

    The human gut microbiome is a dynamic ecosystem where bacteria engage in interspecies competition using molecular weapons such as the type VI secretion system (T6SS). Here, we characterize BteO-BtiO, a unique effector-immunity pair in Bacteroides fragilis that mediates antagonism via a nonenzymatic mechanism. Microscopy reveals that BteO exposure leads to cell elongation, membrane blebbing, and lysis in sensitive strains. Structural and biochemical analyses demonstrate that BteO disrupts cell wall homeostasis by binding to conserved C-terminal domains of OmpA-family proteins (OmpAs), which are critical for outer membrane integrity. The immunity protein BtiO neutralizes BteO by mimicking the OmpA-binding interface. We further show that bile salts enhance BteO-mediated killing in vitro and that BteO confers a competitive advantage in the mammalian gut. Remarkably, BteO exhibits broad-spectrum activity across Bacteroides species. These findings reveal a nonenzymatic strategy of bacterial antagonism and broaden our understanding of T6SS effector diversity within Bacteroides .


  • 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
Major outer membrane protein109Bacteroides fragilis NCTC 9343Mutation(s): 0 
Gene Names: ompABF9343_3708
UniProt
Find proteins for Q5L8U3 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2))
Explore Q5L8U3 
Go to UniProtKB:  Q5L8U3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5L8U3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.369α = 90
b = 44.369β = 90
c = 102.746γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PHENIXphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-10-01 
  • Deposition Author(s): He, J., Gao, X.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references