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- PDB-9ga1: Structure of Pentameric Outer Membrane Protein A from Bdellovibri... -

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Basic information

Entry
Database: PDB / ID: 9ga1
TitleStructure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus
ComponentsMajor outer membrane protein
KeywordsLIPID TRANSPORT / Outer Membrane Protein / Porin / Beta-barel
Function / homologybeta-D-glucopyranose / OCTAN-1-OL / N-OCTANE / PALMITIC ACID / Major outer membrane protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsParr, R.J. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z 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
DepositionJul 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,06828
Polymers181,4025
Non-polymers3,66623
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29130 Å2
ΔGint-23 kcal/mol
Surface area65750 Å2
Unit cell
Length a, b, c (Å)175.430, 191.346, 184.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 9 molecules ABCDE

#1: Protein
Major outer membrane protein


Mass: 36280.457 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 BL21(DE3) (bacteria) / References: UniProt: Q6MQN4
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 314 molecules

#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C8H18
#5: Chemical
ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaCl, 25% v/v pentaerythritol propoxylate (5/4 PO/OH), 10% v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→63.54 Å / Num. obs: 76317 / % possible obs: 99.89 % / Redundancy: 13.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1614 / Rpim(I) all: 0.0448 / Rrim(I) all: 0.1675 / Net I/σ(I): 12.26
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 7548 / CC1/2: 0.871 / CC star: 0.965 / Rpim(I) all: 0.2795 / Rrim(I) all: 1.05 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
DIALSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→63.54 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3737 4.9 %
Rwork0.1977 --
obs0.1998 76238 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→63.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 250 295 13165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813141
X-RAY DIFFRACTIONf_angle_d0.98317756
X-RAY DIFFRACTIONf_dihedral_angle_d10.2751921
X-RAY DIFFRACTIONf_chiral_restr0.0541949
X-RAY DIFFRACTIONf_plane_restr0.0062322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.42991170.33992694X-RAY DIFFRACTION100
2.84-2.870.36391430.29252642X-RAY DIFFRACTION100
2.87-2.910.33941320.28112654X-RAY DIFFRACTION100
2.91-2.950.36461500.25662681X-RAY DIFFRACTION100
2.95-30.30351240.25542638X-RAY DIFFRACTION100
3-3.040.28361290.20452674X-RAY DIFFRACTION100
3.04-3.090.24641310.18622682X-RAY DIFFRACTION100
3.09-3.150.27481330.18452674X-RAY DIFFRACTION100
3.15-3.210.25171250.18842644X-RAY DIFFRACTION100
3.21-3.270.2341210.18522705X-RAY DIFFRACTION100
3.27-3.330.26931220.19532681X-RAY DIFFRACTION100
3.33-3.410.25071280.20152687X-RAY DIFFRACTION100
3.41-3.490.2441370.20732667X-RAY DIFFRACTION100
3.49-3.570.25071310.2162685X-RAY DIFFRACTION100
3.57-3.670.29841390.21942658X-RAY DIFFRACTION100
3.67-3.780.24821420.2052671X-RAY DIFFRACTION100
3.78-3.90.28711470.1942690X-RAY DIFFRACTION100
3.9-4.040.22971460.18542677X-RAY DIFFRACTION100
4.04-4.20.20341430.17112672X-RAY DIFFRACTION100
4.2-4.390.18721480.16432684X-RAY DIFFRACTION100
4.39-4.620.20161510.15692694X-RAY DIFFRACTION100
4.62-4.910.19211590.15642675X-RAY DIFFRACTION100
4.91-5.290.18481720.1592661X-RAY DIFFRACTION100
5.29-5.820.21591350.17012724X-RAY DIFFRACTION100
5.82-6.660.23771270.18582748X-RAY DIFFRACTION100
6.66-8.390.22161540.19382745X-RAY DIFFRACTION100
8.39-63.540.23061510.26592794X-RAY DIFFRACTION98

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