8GRA | pdb_00008gra

Structure of Type VI secretion system cargo delivery vehicle Hcp-VgrG-PAAR


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 362.11 kDa 
  • Atom Count: 20,306 
  • Modeled Residue Count: 2,613 
  • Deposited Residue Count: 3,288 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Type VI secretion system spike protein PaarA [auth J],
K [auth J1],
L [auth J2]
222Bacteroides fragilisMutation(s): 0 
Gene Names: DXA78_05585F2Z89_01155
UniProt
Find proteins for A0A3E5IG32 (Bacteroides fragilis)
Explore A0A3E5IG32 
Go to UniProtKB:  A0A3E5IG32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3E5IG32
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Type VI secretion system spike protein VgrGC [auth I],
D [auth H],
E [auth G]
616Bacteroides fragilisMutation(s): 0 
Gene Names: DXA78_05580F2Z89_01160
UniProt
Find proteins for A0A3E5IG38 (Bacteroides fragilis)
Explore A0A3E5IG38 
Go to UniProtKB:  A0A3E5IG38
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3E5IG38
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072237, 31870132

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-06-25
    Changes: Data collection, Structure summary