9F0Y | pdb_00009f0y

CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the ss-27_+8ds+9_+143-R Locally-refined 3.45 A Map.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history


Literature

Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes.

Williams, S.M.Raffl, S.Kienesberger, S.Ilangovan, A.Zechner, E.L.Waksman, G.

(2025) Nat Commun 16: 4906-4906

  • DOI: https://doi.org/10.1038/s41467-025-60116-6
  • Primary Citation of Related Structures:  
    9F0X, 9F0Y, 9F0Z, 9F10, 9F11, 9F12

  • PubMed Abstract: 

    Bacterial mating, or conjugation, was discovered nearly 80 years ago as a process transferring genes from one bacterial cell (the donor) to another (the recipient). It requires three key multiprotein complexes in the donor cell: a DNA-processing machinery called the relaxosome, a double-membrane spanning type 4 secretion system (T4SS), and an extracellular appendage termed pilus. While the near-atomic resolution structures of the T4SS and pilus are already known, that of the relaxosome has not been reported to date. Here, we describe the cryo-EM structure of the fully assembled relaxosome encoded by the paradigm F plasmid in two different states corresponding to distinct functional steps along the DNA processing reaction. By varying the structures of model DNAs we delineate conformational changes required to initiate conjugation. Mutational studies of the various protein-protein and protein-DNA interaction hubs suggest a complex sensitive to trigger signals, that could arise from cell-to-cell contacts with recipient cells.


  • Organizational Affiliation
    • Institute of Structural and Molecular Biology, School of Natural Sciences, Birkbeck College, Malet Street, London, WC1E 7HX, UK. sunanda.williams@bbk.ac.uk.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit alpha99Escherichia coli K-12Mutation(s): 0 
Gene Names: ihfAhidhimAb1712JW1702
UniProt
Find proteins for P0A6X7 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6X7
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UniProt GroupP0A6X7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Integration host factor subunit beta94Escherichia coli K-12Mutation(s): 0 
Gene Names: ihfBhimDhipb0912JW0895
UniProt
Find proteins for P0A6Y1 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6Y1
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UniProt GroupP0A6Y1
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Relaxosome protein TraYE [auth F],
F [auth E],
G
131Escherichia coli K-12Mutation(s): 0 
Gene Names: traYECOK12F073
UniProt
Find proteins for P06627 (Escherichia coli (strain K12))
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UniProt GroupP06627
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Multifunctional conjugation protein TraI1,763Escherichia coli K-12Mutation(s): 1 
Gene Names: traIECOK12F104
EC: 5.6.2.1 (PDB Primary Data), 3.6.4.12 (PDB Primary Data)
UniProt
Find proteins for P14565 (Escherichia coli (strain K12))
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UniProt GroupP14565
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Entity ID: 1
MoleculeChains LengthOrganismImage
T-strand DNA (95-MER)170Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
R-strand DNA (84-MER)135Escherichia coli K-12
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection