9GF0 | pdb_00009gf0

Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily.

Parr, R.J.Santin, Y.G.Ratkeviciute, G.Caulton, S.G.Radford, P.Gurvic, D.Jenkins, M.Doyle, M.T.Mead, L.Silale, A.van den Berg, B.Knowles, T.J.Sockett, R.E.Stansfeld, P.J.Laloux, G.Lovering, A.L.

(2025) Nat Commun 16: 6213-6213

  • DOI: https://doi.org/10.1038/s41467-025-61633-0
  • Primary Citation of Related Structures:  
    9GA1, 9GF0

  • PubMed Abstract: 

    Outer membrane proteins (OMPs) define the surface biology of Gram-negative bacteria, with roles in adhesion, transport, catalysis and signalling. Specifically, porin beta-barrels are common diffusion channels, predominantly monomeric/trimeric in nature. Here we show that the major OMP of the bacterial predator Bdellovibrio bacteriovorus, PopA, differs from this architecture, forming a pentameric porin-like superstructure. Our X-ray and cryo-EM structures reveal a bowl-shape composite outer β-wall, which houses a central chamber that encloses a section of the lipid bilayer. We demonstrate that PopA, reported to insert into prey inner membrane, causes defects when directed into Escherichia coli membranes. We discover widespread PopA homologues, including likely tetramers and hexamers, that retain the lipid chamber; a similar chamber is formed by an unrelated smaller closed-barrel family, implicating this as a general feature. Our work thus defines oligomeric OMP superfamilies, whose deviation from prior structures requires us to revisit existing membrane-interaction motifs and folding models.


  • Organizational Affiliation

    School of Biosciences, University of Birmingham, Birmingham, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major outer membrane protein
A, B, C, D, E
344Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd0427
UniProt
Find proteins for Q6MQN4 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MQN4 
Go to UniProtKB:  Q6MQN4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MQN4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom209437/Z/17/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M01116X/1
Medical Research Council (MRC, United Kingdom)United KingdomMC_PC_17136

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references