7YW0

Bacteroides fragilis Hcp5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and assembly of type VI secretion system cargo delivery vehicle.

He, W.Wu, K.Ouyang, Z.Bai, Y.Luo, W.Wu, D.An, H.Guo, Y.Jiao, M.Qin, Q.Zhang, J.Wu, Y.She, J.Hwang, P.M.Zheng, F.Zhu, L.Wen, Y.

(2023) Cell Rep 42: 112781-112781

  • DOI: https://doi.org/10.1016/j.celrep.2023.112781
  • Primary Citation of Related Structures:  
    7YW0, 8GRA

  • PubMed Abstract: 

    Type VI secretion system is widely used in Gram-negative bacteria for injecting toxic effectors into neighboring prokaryotic or eukaryotic cells. Various effectors can be loaded onto the T6SS delivery tube via its core components: Hcp, VgrG, or PAAR. Here, we report 2.8-Å resolution cryo-EM structure of intact T6SS Hcp5-VgrG-PAAR cargo delivery system and crystal structure of unbound Hcp5 from B. fragilis NCTC 9343. Loading of Hcp5 hexameric ring onto VgrG causes expansion of its inner cavity and external surface, explaining how structural changes could be propagated to regulate co-polymerization and surrounding contractile sheath. High-affinity binding between Hcp and VgrG causes entropically unfavorable structuring of long loops. Furthermore, interactions between VgrG trimer and Hcp hexamer are asymmetric, with three of the six Hcp monomers exhibiting a major loop flip. Our study provides insights into the assembly, loading, and firing of T6SS nanomachine that contributes to bacterial inter-species competition and host interactions.


  • Organizational Affiliation

    Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterodales T6SS protein TssD (Hcp)
A, B
129Bacteroides fragilisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for A0A081TQ32 (Bacteroides fragilis)
Explore A0A081TQ32 
Go to UniProtKB:  A0A081TQ32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A081TQ32
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.238 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.102α = 90
b = 77.102β = 90
c = 79.491γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870132

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release