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- EMDB-51308: Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bde... -

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Basic information

Entry
Database: EMDB / ID: EMD-51308
TitleCryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus
Map dataOverall Map
Sample
  • Complex: Pentameric Outer Membrane protein A, PopA
    • Protein or peptide: Major outer membrane protein
  • Ligand: water
KeywordsOuter membrane protein / porin / beta-barrel / LIPID BINDING PROTEIN
Function / homologyMajor outer membrane protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsParr RJ / Ratkeviciute G / Lovering AL
Funding support United Kingdom, 3 items
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, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51308.png

Downloads & links

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Map

FileDownload / File: emd_51308.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.0763147 - 1.5214568
Average (Standard dev.)0.0011521117 (±0.041213065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51308_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_51308_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51308_half_map_2.map
Projections & Slices
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Sample components

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Entire : Pentameric Outer Membrane protein A, PopA

EntireName: Pentameric Outer Membrane protein A, PopA
Components
  • Complex: Pentameric Outer Membrane protein A, PopA
    • Protein or peptide: Major outer membrane protein
  • Ligand: water

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Supramolecule #1: Pentameric Outer Membrane protein A, PopA

SupramoleculeName: Pentameric Outer Membrane protein A, PopA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bdellovibrio bacteriovorus HD100 (bacteria)

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Macromolecule #1: Major outer membrane protein

MacromoleculeName: Major outer membrane protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Bdellovibrio bacteriovorus HD100 (bacteria)
Molecular weightTheoretical: 37.092637 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKARVEALAN SRHVLDFQTA FDRPYQFMAL SEQATIEWGN TGDANPHAEG GFVKRHGDDS AFGAYFGRRS ADFSEAVQTV RDASSHHHH HHGSSNPAFA DLMFEQNGLN LFYASKMGEW TWGVTAKYSN GKNEDPTVGT KATSAGVAVA ASNGTWDFEL V QGFTGKSE ...String:
SKARVEALAN SRHVLDFQTA FDRPYQFMAL SEQATIEWGN TGDANPHAEG GFVKRHGDDS AFGAYFGRRS ADFSEAVQTV RDASSHHHH HHGSSNPAFA DLMFEQNGLN LFYASKMGEW TWGVTAKYSN GKNEDPTVGT KATSAGVAVA ASNGTWDFEL V QGFTGKSE LDNGTVTAEV ESKGLTNVTV GYHMSPEMEV YGNVKMSKVE ADLNGTPIEV ETTSYKVGMV NTLAKSEEGN FF YGVEVAS TKVKDDSESL LLPVYMGVEH NAASWLVLRA SVAQNVILNE TKDDATGNKT DEDSTRMAAG AGIKFGKSVI DAS FAGSTT GVINANNLFS QVAYTYTF

UniProtKB: Major outer membrane protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 33 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium ChlorideNaCl
0.03 (w/v) %n-dodecyl-beta-D-maltoside (DDM)C24H46O11
GridModel: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 992500
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Software - details: Punjani et al., 2017 / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-inition
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 365835
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Crystallographic stucture
RefinementProtocol: OTHER
Output model

PDB-9gf0:
Cryo-EM Structure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus

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