6U9E

Structure of PdpA-VgrG Complex, Lidless


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic Structure of the Francisella T6SS Central Spike Reveals a Unique alpha-Helical Lid and a Putative Cargo.

Yang, X.Clemens, D.L.Lee, B.Y.Cui, Y.Zhou, Z.H.Horwitz, M.A.

(2019) Structure 27: 1811-1819.e6

  • DOI: https://doi.org/10.1016/j.str.2019.10.007
  • Primary Citation of Related Structures:  
    6U9E, 6U9F, 6U9G

  • PubMed Abstract: 

    Francisella bacteria rely on a phylogenetically distinct type VI secretion system (T6SS) to escape host phagosomes and cause the fatal disease tularemia, but the structural and molecular mechanisms involved are unknown. Here we report the atomic structure of the Francisella T6SS central spike complex, obtained by cryo-electron microscopy. Our structural and functional studies demonstrate that, unlike the single-protein spike composition of other T6SS subtypes, Francisella T6SS's central spike is formed by two proteins, PdpA and VgrG, akin to T4-bacteriophage gp27 and gp5, respectively, and that PdpA has unique characteristics, including a putative cargo within its cavity and an N-terminal helical lid. Structure-guided mutagenesis demonstrates that the PdpA N-terminal lid and C-terminal spike are essential to Francisella T6SS function. PdpA is thus both an adaptor, connecting VgrG to the tube, and a likely carrier of secreted cargo. These findings are important to understanding Francisella pathogenicity and designing therapeutics to combat tularemia.


  • Organizational Affiliation

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PdpAA,
B [auth C],
C [auth E]
820Francisella tularensis subsp. novicidaMutation(s): 0 
Gene Names: pdpA
UniProt
Find proteins for Q7X3I9 (Francisella novicida)
Explore Q7X3I9 
Go to UniProtKB:  Q7X3I9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7X3I9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VgrGD [auth B],
E [auth D],
F
189Francisella tularensis subsp. novicidaMutation(s): 0 
Gene Names: B4919_03525
UniProt
Find proteins for Q7X3I8 (Francisella novicida)
Explore Q7X3I8 
Go to UniProtKB:  Q7X3I8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7X3I8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.21 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesAI125497

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references