9MOQ | pdb_00009moq

Cryo-EM of F-pilus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the conjugation H-pilus reveals the cyclic nature of the TrhA pilin.

Ishimoto, N.Wong, J.L.C.He, S.Shirran, S.Wright-Paramio, O.Seddon, C.Singh, N.Balsalobre, C.Sonani, R.R.Clements, A.Egelman, E.H.Frankel, G.Beis, K.

(2025) Proc Natl Acad Sci U S A 122: e2427228122-e2427228122

  • DOI: https://doi.org/10.1073/pnas.2427228122
  • Primary Citation of Related Structures:  
    9HVC, 9MOQ

  • PubMed Abstract: 

    Conjugation, the major driver of the spread of antimicrobial resistance genes, relies on a conjugation pilus for DNA transfer. Conjugative pili, such as the F-pilus, are dynamic tubular structures, composed of a polymerized pilin, that mediate the initial donor-recipient interactions, a process known as mating pair formation (MPF). IncH are low-copy-number plasmids, traditionally considered broad host range, which are found in bacteria infecting both humans and animals. The reference IncHI1 plasmid R27, isolated from Salmonella enterica serovar Typhi, encodes the conjugative H-pilus subunit TrhA containing 74 residues after cleavage of the signal sequence. Here, we show that the H-pilus forms long filamentous structures that mediate MPF and describe its cryoelectron-microscopic (cryo-EM) structure at 2.2 Å resolution. Like the F pilus, the H-pilin subunits form helical assemblies with phospholipid molecules at a stoichiometric ratio of 1:1. While there were previous reports that the T-pilus from Agrobacterium tumefaciens was composed of cyclic subunits, three recent cryo-EM structures of the T-pilus found no such cyclization. Here, we report that the H-pilin is cyclic, with a covalent bond connecting the peptide backbone between the N and C termini. Both the cryo-EM map and mass spectrometry revealed cleavage of the last five residues of the pilin, followed by cyclization via condensation of the amine and carboxyl residues. Mutagenesis experiments revealed that loss of cyclization abolished pilus biogenesis and efficient plasmid transfer. The cyclic nature of the pilin could stabilize the pilus and may explain the high incidence of IncH plasmid dissemination.


  • Organizational Affiliation
    • Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot Oxfordshire OX11 0FA, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pilin121Escherichia coliMutation(s): 0 
UniProt
Find proteins for P04737 (Escherichia coli (strain K12))
Explore P04737 
Go to UniProtKB:  P04737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04737
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X41 (Subject of Investigation/LOI)
Query on X41

Download Ideal Coordinates CCD File 
B [auth A]1-MYRISTOYL-2-MYRISTOLEOYL-SN-GLYCERO-3-PHOSPHATE
C31 H58 O8 P
GVANAVLIALOKCA-HQGHLRICSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.15.2_3472:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2026-01-28
    Changes: Data collection, Database references