8YPT

Cryo-EM structure of BfUbb-ButCD complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A highly conserved SusCD transporter determines the import and species-specific antagonism of Bacteroides ubiquitin homologues.

Tong, M.Xu, J.Li, W.Jiang, K.Yang, Y.Chen, Z.Jiao, X.Meng, X.Wang, M.Hong, J.Long, H.Liu, S.J.Lim, B.Gao, X.

(2024) Nat Commun 15: 8794-8794

  • DOI: https://doi.org/10.1038/s41467-024-53149-w
  • Primary Citation of Related Structures:  
    8YPT, 8YPU

  • PubMed Abstract: 

    Efficient interbacterial competitions and diverse defensive strategies employed by various bacteria play a crucial role in acquiring a hold within a dense microbial community. The gut symbiont Bacteroides fragilis secretes an antimicrobial ubiquitin homologue (BfUbb) that targets an essential periplasmic PPIase to drive intraspecies bacterial competition. However, the mechanisms by which BfUbb enters the periplasm and its potential for interspecies antagonism remain poorly understood. Here, we employ transposon mutagenesis and identify a highly conserved TonB-dependent transporter SusCD (designated as ButCD) in B. fragilis as the BfUbb transporter. As a putative protein-related nutrient utilization system, ButCD is widely distributed across diverse Bacteroides species with varying sequence similarity, resulting in distinct import efficiency of Bacteroides ubiquitin homologues (BUbb) and thereby determining the species-specific toxicity of BUbb. Cryo-EM structural and functional investigations of the BfUbb-ButCD complex uncover distinctive structural features of ButC that are crucial for its targeting by BfUbb. Animal studies further demonstrate the specific and efficient elimination of enterotoxigenic B. fragilis (ETBF) in the murine gut by BfUbb, suggesting its potential as a therapeutic against ETBF-associated inflammatory bowel disease and colorectal cancer. Our findings provide a comprehensive elucidation of the species-specific toxicity exhibited by BUbb and explore its potential applications.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane protein
A, B
423Bacteroides fragilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q64UE3 (Bacteroides fragilis (strain YCH46))
Explore Q64UE3 
Go to UniProtKB:  Q64UE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64UE3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TonB-linked outer membrane protein
C, D
986Bacteroides fragilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q64UE4 (Bacteroides fragilis (strain YCH46))
Explore Q64UE4 
Go to UniProtKB:  Q64UE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64UE4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein76Bacteroides fragilisMutation(s): 0 
Gene Names: O1404_18505
UniProt
Find proteins for Q5L8M7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2))
Explore Q5L8M7 
Go to UniProtKB:  Q5L8M7
Entity Groups  
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UniProt GroupQ5L8M7
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-25
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection
  • Version 1.3: 2024-11-27
    Changes: Data collection