6GYB

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri.

Sgro, G.G.Costa, T.R.D.Cenens, W.Souza, D.P.Cassago, A.Coutinho de Oliveira, L.Salinas, R.K.Portugal, R.V.Farah, C.S.Waksman, G.

(2018) Nat Microbiol 3: 1429-1440

  • DOI: https://doi.org/10.1038/s41564-018-0262-z
  • Primary Citation of Related Structures:  
    6GYB

  • PubMed Abstract: 

    Type IV secretion (T4S) systems form the most common and versatile class of secretion systems in bacteria, capable of injecting both proteins and DNAs into host cells. T4S systems are typically composed of 12 components that form 2 major assemblies: the inner membrane complex embedded in the inner membrane and the core complex embedded in both the inner and outer membranes. Here we present the 3.3 Å-resolution cryo-electron microscopy model of the T4S system core complex from Xanthomonas citri, a phytopathogen that utilizes this system to kill bacterial competitors. An extensive mutational investigation was performed to probe the vast network of protein-protein interactions in this 1.13-MDa assembly. This structure expands our knowledge of the molecular details of T4S system organization, assembly and evolution.


  • Organizational Affiliation

    Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VirB7139Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: XAC2622
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VirB9 protein255Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: virB9XAC2620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VirB10 protein406Xanthomonas citri pv. citri str. 306Mutation(s): 0 
Gene Names: virB10XAC2619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX1.12

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098302
Sao Paulo Research FoundationBrazil2011/07777-5
Sao Paulo Research FoundationBrazil2017/17303-7

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other