9VF4 | pdb_00009vf4

CryoEM structure of phospholipid-independent cyclised RP4 pilus

• PDB DOI: https://doi.org/10.2210/pdb9VF4/pdb
• EM Map EMD-65024: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-10 Released: 2026-05-27 
• Deposition Author(s): Ishimoto, N., Beis, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Phospholipid-independent biogenesis and function of the RP4 conjugation pilus.

Ishimoto, N., He, S., Bogdanov, M., Smith, T.K., Frankel, G., Beis, K.

(2026) Nat Commun 

• PubMed: 42310306 
• DOI: https://doi.org/10.1038/s41467-026-74409-x
• Primary Citation Related Structures: 
  9VF4


• PubMed Abstract: 
  

  Bacterial conjugation, the process of horizontal gene transfer between bacteria, is initiated by mating pair formation (MPF) via a conjugative pilus. Conjugation of the IncP RP4 plasmid is mediated by short mating pili. Here, we report the cryo-EM structure of the RP4 pilus at 2.74 Å resolution. Uniquely, both the structural and quantitative mass spectral analyses revealed that the cyclic TrbC pilin subunit is not lipidated. Consistently, an E. coli pgsA mutant lacking phosphatidylglycerol (PG) can serve as a donor of RP4 but not of F- (pKpQIL), H- (R27) or W- (R388) pili, whose biogenesis and DNA transfer is PG-dependent. RP4 is the first example of a lipid-independent functional mating pilus. This discovery suggests that an amphipathic lipid moiety is not universally essential for the biogenesis of conjugative pili and MPF, providing an alternative model for their assembly and function. These data expand our understanding of the diverse bacterial mechanisms employ to transfer genetic material.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College London, London, UK.
Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK.
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan.
Department of Biochemistry & Molecular Biology, University of Texas-Houston, McGovern Medical School, Fannin, USA.
BSRC, Schools of Biology and Chemistry, University of St Andrews, St Andrews, UK.
Department of Life Sciences, Imperial College London, London, UK. [e-mail].
Department of Life Sciences, Imperial College London, London, UK. [e-mail].
Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 55-mer - A55 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 8.14 kDa 
• Atom Count: 574 
• Modeled Residue Count: 78 
• Deposited Residue Count: 78 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TrbC/VIRB2 family protein	A [auth c]	78	Escherichia coli	Mutation(s): 0  Gene Names: p482-1_00154, p492-9_00169
UniProt
Find proteins for A0A2R4AH65 (Escherichia coli) Explore A0A2R4AH65  Go to UniProtKB:  A0A2R4AH65

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.74 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Ishimoto, N., Beis, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release
  
• Version 1.1: 2026-07-01
  Changes: Data collection, Database references