9VP2 | pdb_00009vp2

CryoEM structure of cyclised H-pilus (D69A)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 9VP2

This is version 1.2 of the entry. See complete history

Literature

H pilin cyclisation and pilus biogenesis are promiscuous but electrostatic perturbations impair conjugation efficiency.

He, S.Ishimoto, N.Wong, J.L.C.David, S.Sanchez-Garrido, J.Bogdanov, M.Beis, K.Frankel, G.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-69599-3
  • Primary Citation Related Structures: 
    9VP2, 9VP3, 9VP4, 9VPE

  • PubMed Abstract: 

    During conjugation, plasmid DNA is transferred from donor to recipient bacteria via the plasmid-encoded mating pilus, formed as thin helical assemblies of polymerised pilin subunits. In the IncHI1 R27 plasmid-encoded pilus, the TrhA pilin undergoes cyclisation (via a peptide bond between Gly1 and Asp69), essential for conjugation. Gly1 and Asp69 are exposed on the pilus surface and conserved in all TrhA pilins in the Plascad database. Substituting Asp69 with Asn, Ala, Gly, or Arg does not prevent cyclisation or pilus formation, which remains structurally indistinguishable from the wild type. Conjugation efficiency of the Asp69 substitutions across multiple recipient species correlates with side chain size, in the order Asp69Asn > Asp69Ala > Asp69Gly. However, Asp69Arg, as well as Asp69Lys and Gly1Lys substitutions abolish conjugation, likely due to the positively charged pilus surface (opposite to the wild-type negative charge) forming unfavourable electrostatic interactions with the recipient outer membrane's inner leaflet, composed solely of zwitterionic phosphatidylethanolamine (PE). Consistently, conjugation is rescued in recipients lacking PE. These findings indicate strong selective pressure to maintain Gly1 and Asp69, as efficient DNA transfer depends on precise electrostatic and steric constraints of the pilus surface.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, London, UK.

Macromolecule Content 

  • Total Structure Weight: 8.28 kDa 
  • Atom Count: 544 
  • Modeled Residue Count: 69 
  • Deposited Residue Count: 74 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Pilin74Salmonella enterica subsp. enterica serovar TyphiMutation(s): 1 
Gene Names: trhAHCM1.67
UniProt
Find proteins for Q935P5 (Salmonella typhi)
Explore Q935P5 
Go to UniProtKB:  Q935P5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ935P5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
B [auth A]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references
  • Version 1.2: 2026-04-08
    Changes: Data collection, Database references