6GYB | pdb_00006gyb

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

• PDB DOI: https://doi.org/10.2210/pdb6GYB/pdb
• EM Map EMD-0089: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Xanthomonas citri subsp. citri 306
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-28 Released: 2018-10-24 
• Deposition Author(s): Sgro, G.G., Costa, T.R.D., Farah, C.S., Waksman, G.
• Funding Organization(s): Wellcome Trust, Sao Paulo Research Foundation

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Experimental Data Snapshot

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

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

• PubMed: 30349081 
• DOI: https://doi.org/10.1038/s41564-018-0262-z
• Primary Citation 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.

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Organizational Affiliation: 
• Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
Institute of Structural and Molecular Biology at UCL and Birkbeck College, Department of Biological Sciences, Birkbeck College, London, UK.
MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.
MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, Brazil.
Department of Medicinal Chemistry, Université du Québec, INRS - Institut Armand-Frappier, Laval, Québec, Canada.
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil. [e-mail].
Institute of Structural and Molecular Biology at UCL and Birkbeck College, Department of Biological Sciences, Birkbeck College, London, UK. [e-mail].
Institute of Structural and Molecular Biology at UCL and Birkbeck College, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C14  (Explore in 3D)
Global Stoichiometry: Hetero 42-mer - A14B14C14 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 1,225.21 kDa 
• Atom Count: 59,318 
• Modeled Residue Count: 7,546 
• Deposited Residue Count: 11,200 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VirB7	A [auth a], BA [auth G], D [auth d], EA [auth J], G [auth g], HA [auth M], J [auth j], KA [auth P], M [auth m], NA [auth S], P [auth p], S [auth s], V [auth A], Y [auth D]	139	Xanthomonas citri subsp. citri 306	Mutation(s): 0  Gene Names: XAC2622

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VirB9 protein	B [auth b], CA [auth H], E [auth e], FA [auth K], H [auth h], IA [auth N], K [auth k], LA [auth Q], N [auth n], OA [auth T], Q [auth q], T [auth t], W [auth B], Z [auth E]	255	Xanthomonas citri subsp. citri 306	Mutation(s): 0  Gene Names: virB9, XAC2620

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VirB10 protein	AA [auth F], C [auth c], DA [auth I], F [auth f], GA [auth L], I [auth i], JA [auth O], L [auth l], MA [auth R], O [auth o], PA [auth U], R [auth r], U [auth u], X [auth C]	406	Xanthomonas citri subsp. citri 306	Mutation(s): 0  Gene Names: virB10, XAC2619

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	1.12

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-24 
Deposition Author(s): Sgro, G.G., Costa, T.R.D., Farah, C.S., Waksman, G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	098302
Sao Paulo Research Foundation	Brazil	2011/07777-5
Sao Paulo Research Foundation	Brazil	2017/17303-7

Revision History  

• 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
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Structure summary