9GA1 | pdb_00009ga1

Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.239 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
333Bdellovibrio 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
O [auth C],
U [auth D],
Z [auth E]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
BGC
Query on BGC

Download Ideal Coordinates CCD File 
BA [auth E],
J [auth A],
N [auth B],
X [auth D]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
OC9
Query on OC9

Download Ideal Coordinates CCD File 
AA [auth E],
K [auth A],
R [auth C],
W [auth D]
OCTAN-1-OL
C8 H18 O
KBPLFHHGFOOTCA-UHFFFAOYSA-N
OCT
Query on OCT

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
M [auth B]
P [auth C]
G [auth A],
H [auth A],
I [auth A],
M [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth D],
Y [auth E]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.239 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.43α = 90
b = 191.346β = 90
c = 184.313γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
DIALSdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom209437/Z/17/Z

Revision History  (Full details and data files)

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