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- PDB-9gf0: Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bde... -

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Basic information

Entry
Database: PDB / ID: 9gf0
TitleCryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus
ComponentsMajor outer membrane protein
KeywordsLIPID BINDING PROTEIN / Outer membrane protein / porin / beta-barrel
Function / homologyMajor outer membrane protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsParr, R.J. / Ratkeviciute, G. / Lovering, A.L.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M01116X/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17136 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily.
Authors: Rebecca J Parr / Yoann G Santin / Giedrė Ratkevičiūte / Simon G Caulton / Paul Radford / Dominik Gurvič / Matthew Jenkins / Matthew T Doyle / Liam Mead / Augustinas Silale / Bert van den ...Authors: Rebecca J Parr / Yoann G Santin / Giedrė Ratkevičiūte / Simon G Caulton / Paul Radford / Dominik Gurvič / Matthew Jenkins / Matthew T Doyle / Liam Mead / Augustinas Silale / Bert van den Berg / Timothy J Knowles / R Elizabeth Sockett / Phillip J Stansfeld / Géraldine Laloux / Andrew L Lovering /
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 ...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.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major outer membrane protein
B: Major outer membrane protein
C: Major outer membrane protein
D: Major outer membrane protein
E: Major outer membrane protein


Theoretical massNumber of molelcules
Total (without water)185,4635
Polymers185,4635
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Major outer membrane protein


Mass: 37092.637 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd0427 / Production host: Escherichia coli (E. coli) / Strain (production host): D42 / References: UniProt: Q6MQN4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pentameric Outer Membrane protein A, PopA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bdellovibrio bacteriovorus HD100 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: D43
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMSodium ChlorideNaCl1
30.03 (w/v) %n-dodecyl-beta-D-maltoside (DDM)C24H46O111
SpecimenConc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GRAPHENE OXIDE / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 55.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selectionPunjani et al., 2017
4cryoSPARC4.4.1CTF correctionPunjani et al., 2017
7UCSF ChimeraX1.4model fittingPettersen EF, et al. 2021
13PHENIX1.2.1model refinementAfonine PV, et al. 2018
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 992500
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 365835 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Atomic model buildingDetails: Crystallographic stucture / Source name: Other / Type: other

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