8RTD

Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis.

Mace, K.Waksman, G.

(2024) EMBO J 

  • DOI: https://doi.org/10.1038/s44318-024-00135-z
  • Primary Citation of Related Structures:  
    8RT4, 8RT5, 8RT6, 8RT7, 8RT8, 8RT9, 8RTA, 8RTB, 8RTD

  • PubMed Abstract: 

    Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow 2009; Virolle et al, 2020). Conjugative T4SSs form pili: long extracellular filaments that connect with recipient cells. Previously, we solved the cryo-electron microscopy (cryo-EM) structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a fourth VirB8 subunit in the asymmetric unit of both the arches and the inner membrane complex (IMC), and a hydrophobic VirB5 tip in the distal end of the stalk. Additionally, we provide previously undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK. kevin.mace@univ-rennes.fr.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TrwJ proteinA,
C [auth B],
E [auth C],
G [auth K],
I [auth E]
229Escherichia coliMutation(s): 0 
Gene Names: trwJ
Membrane Entity: Yes 
UniProt
Find proteins for A8R752 (Salmonella dublin)
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Go to UniProtKB:  A8R752
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UniProt GroupA8R752
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TrwG protein231Escherichia coliMutation(s): 0 
Gene Names: trwG
Membrane Entity: Yes 
UniProt
Find proteins for A8R756 (Salmonella dublin)
Explore A8R756 
Go to UniProtKB:  A8R756
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UniProt GroupA8R756
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TrwE proteinDA [auth e],
H [auth a],
Z
395Escherichia coliMutation(s): 0 
Gene Names: trwE
Membrane Entity: Yes 
UniProt
Find proteins for A8R758 (Salmonella dublin)
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Go to UniProtKB:  A8R758
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UniProt GroupA8R758
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
TrwI proteinJ [auth L],
K [auth M],
M [auth H],
O [auth I],
Q [auth J]
342Escherichia coliMutation(s): 0 
Gene Names: trwI
Membrane Entity: Yes 
UniProt
Find proteins for A8R754 (Salmonella dublin)
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Go to UniProtKB:  A8R754
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UniProt GroupA8R754
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
TrwM proteinEA [auth f],
L [auth j],
S [auth R]
104Escherichia coliMutation(s): 0 
Gene Names: trwM
Membrane Entity: Yes 
UniProt
Find proteins for A8R750 (Salmonella dublin)
Explore A8R750 
Go to UniProtKB:  A8R750
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UniProt GroupA8R750
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Type IV secretion system protein virB4823Escherichia coliMutation(s): 0 
Gene Names: trwK
UniProt
Find proteins for A8R751 (Salmonella dublin)
Explore A8R751 
Go to UniProtKB:  A8R751
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UniProt GroupA8R751
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.33 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom098302
Wellcome TrustUnited Kingdom217089
Wellcome TrustUnited Kingdom202679/Z/16/Z
Wellcome TrustUnited Kingdom206166/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-07-03
    Changes: Data collection, Database references