7FCF

Crystal structure of T6SS Hcp protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Bacterial antagonism of Chromobacterium haemolyticum and characterization of its putative type VI secretion system.

Zwe, Y.H.Yadav, M.Ten, M.M.Z.Srinivasan, M.Jobichen, C.Sivaraman, J.Li, D.

(2022) Res Microbiol 173: 103918-103918

  • DOI: https://doi.org/10.1016/j.resmic.2021.103918
  • Primary Citation of Related Structures:  
    7FCF

  • PubMed Abstract: 

    This study reports the isolation of a new Chromobacterium haemolyticum strain named WI5 from a hydroponic farming facility. WI5 exhibited remarkable bacterial antagonistic properties, eliminating Salmonella, Escherichia coli, Listeria monocytogenes and Staphylococcus aureus (initial inoculum load ∼10 5  CFU/ml) in dual-species co-culture biofilms. Antagonism was strictly contact-dependent and highly influenced by nutrient availability. Next, we identified a complete suite of putative Type VI secretion system (T6SS) genes in the WI5 genome, annotated the gene locus architecture, and determined the crystal structure of hallmark T6SS tube protein Hcp1, which revealed a hexameric ring structure with an outer and inner diameter of 77 and 45 Å, respectively. Structural comparison with homologs showed differences in the key loops connecting the β-strands in which the conserved residues are located, suggesting a role of these residues in the protein function. The T6SS is well-known to facilitate interbacterial competition, and the putative T6SS characterized herein might be responsible for the remarkable antagonism by C. haemolyticum WI5. Collectively, these findings shed light on the nature of bacterial antagonism and a putative key virulence determinant of C. haemolyticum, which might aid in further understanding its potential ecological role in natural habitats.


  • Organizational Affiliation

    Department of Food Science & Technology, 2 Science Drive 2, Faculty of Science, National University of Singapore, Singapore, 117543.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fimbrial protein154Chromobacterium haemolyticumMutation(s): 0 
Gene Names: B0T39_16745
UniProt
Find proteins for A0A1W0CP47 (Chromobacterium haemolyticum)
Explore A0A1W0CP47 
Go to UniProtKB:  A0A1W0CP47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W0CP47
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fimbrial protein
B, C, D, E, F
163Chromobacterium haemolyticumMutation(s): 0 
Gene Names: B0T39_16745
UniProt
Find proteins for A0A1W0CP47 (Chromobacterium haemolyticum)
Explore A0A1W0CP47 
Go to UniProtKB:  A0A1W0CP47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W0CP47
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.205α = 90
b = 83.151β = 90
c = 156.083γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description