9F11 image
Deposition Date 2024-04-17
Release Date 2025-06-04
Last Version Date 2025-07-09
Entry Detail
PDB ID:
9F11
Title:
CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI its TE mode, derived from ss-27_+3ds+4_+143-R Locally-refined 3.68 A Map.
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.68 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polydeoxyribonucleotide
Molecule:T-strand DNA (96-MER)
Chain IDs:A
Chain Length:170
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polydeoxyribonucleotide
Molecule:R-strand DNA (85-MER)
Chain IDs:B
Chain Length:140
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Integration host factor subunit alpha
Gene (Uniprot):ihfA
Chain IDs:C
Chain Length:99
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Integration host factor subunit beta
Gene (Uniprot):ihfB
Chain IDs:D
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Relaxosome protein TraY
Gene (Uniprot):traY
Chain IDs:E, F, G
Chain Length:131
Number of Molecules:3
Biological Source:Escherichia coli K-12
Polymer Type:polypeptide(L)
Molecule:Multifunctional conjugation protein TraI
Gene (Uniprot):traI
Mutations:Y16F single-point mutation, MEFELGT introduced during cloning
Chain IDs:H
Chain Length:1763
Number of Molecules:1
Biological Source:Escherichia coli K-12
Ligand Molecules
Primary Citation
Cryo-EM Structure of the relaxosome, a complex essential for bacterial mating and the spread of antibiotic resistance genes.
Nat Commun 16 4906 4906 (2025)
PMID: 40425557 DOI: 10.1038/s41467-025-60116-6

Abstact

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.

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Primary Citation of related structures