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- PDB-9pxg: Cryo-EM structure of apo BAM from P. aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 9pxg
TitleCryo-EM structure of apo BAM from P. aeruginosa PAO1
Components(Outer membrane protein assembly factor ...) x 5
KeywordsMEMBRANE PROTEIN / protein complex / outer membrane / beta-barrel / protein folding / Gram-negative bacterial protein
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity
Similarity search - Function
Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein ...Outer membrane protein assembly factor BamB / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC, C-terminal / Outer membrane protein assembly factor BamC-like C-terminal domain / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamB / BamE-like / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMunder, F. / Venugopal, H. / Grinter, R.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102150 Australia
CitationJournal: Nat Commun / Year: 2026
Title: L-type pyocins inhibit the BAM complex to kill without cell entry.
Authors: Fabian Munder / Matthew D Johnson / Imogen Samuels / Laura McCaughey / Oleksii Zdorevskyi / Chunxiao Wang / Ashleigh Kropp / Lauren Zavan / Erin P Price / Derek S Sarovich / Swati Varshney / ...Authors: Fabian Munder / Matthew D Johnson / Imogen Samuels / Laura McCaughey / Oleksii Zdorevskyi / Chunxiao Wang / Ashleigh Kropp / Lauren Zavan / Erin P Price / Derek S Sarovich / Swati Varshney / Christopher A McDevitt / Hari Venugopal / Vivek Sharma / Matthew T Doyle / Francesca Short / Debnath Ghosal / James P R Connolly / Gavin J Knott / Rhys Grinter /
Abstract: Many antibiotics are ineffective against the Gram-negative pathogen Pseudomonas aeruginosa because of intrinsic defence mechanisms, such as the impermeable bacterial outer membrane. Here, we show ...Many antibiotics are ineffective against the Gram-negative pathogen Pseudomonas aeruginosa because of intrinsic defence mechanisms, such as the impermeable bacterial outer membrane. Here, we show that protein antibiotics called L-type pyocins kill P. aeruginosa by inhibiting the β-barrel assembly machinery (BAM) complex at the cell surface, halting outer-membrane protein assembly. Using single-particle cryo-electron microscopy, we show that L-type pyocins bind a surface-exposed region of BamA and deploy a C-terminal peptide that competitively inhibits the BAM complex, demonstrating that cell entry is not required for antibiotic activity. We combine genetics, multi-omics and cryo-electron tomography to show that BAM complex inhibition by L-type pyocins or the cyclic-peptide antibiotic, darobactin, triggers a multifaceted transcriptomic, proteomic, and morphological response. BAM inhibition ultimately leads to a catastrophic loss of membrane integrity and cell death. These results validate BAM as a target for antibiotics that do not enter the cell and define an engineerable system for their development.
History
DepositionAug 5, 2025Deposition site: RCSB / Processing site: RCSB
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: Outer membrane protein assembly factor BamB
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,8926
Polymers233,8695
Non-polymers231
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Outer membrane protein assembly factor ... , 5 types, 5 molecules ABCDE

#1: Protein Outer membrane protein assembly factor BamA


Mass: 92258.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXY4
#2: Protein Outer membrane protein assembly factor BamB


Mass: 40436.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9HXJ7
#3: Protein Outer membrane protein assembly factor BamC


Mass: 43100.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: Q9I4W2
#4: Protein Outer membrane protein assembly factor BamD


Mass: 38660.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: P33641
#5: Protein Outer membrane protein assembly factor BamE


Mass: 19411.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) / References: UniProt: O68562

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Details

Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1PAO1-BAMCOMPLEXBAM complex natively purified from P. aeruginosa PAO1#1-#50NATURAL
2BamACOMPLEXBamA subunit of the BAM complex#11NATURAL
3BamBCOMPLEXBamb of the BAM complex#21NATURAL
4BamCCOMPLEXBamC of the BAM complex#31NATURAL
5BamDCOMPLEXBamD of the BAM complex#41NATURAL
6BamECOMPLEXBamE of the BAM complex#51NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.230 MDaNO
210.087 MDaNO
310.04 MDaNO
410.043 MDaNO
510.038 MDaNO
610.019 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Pseudomonas aeruginosa (bacteria)287PAO1
32Pseudomonas aeruginosa (bacteria)287PAO1
43Pseudomonas aeruginosa (bacteria)287PAO1
54Pseudomonas aeruginosa (bacteria)287PAO1
65Pseudomonas aeruginosa (bacteria)287PAO1
76Pseudomonas aeruginosa (bacteria)287PAO1
Buffer solutionpH: 8
Details: Buffer originally contained 0.01 % LMNG, but before grid preparation, LMNG concentration was removed by dilution and re-concentrating in 100 kDa concentrators
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 2.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.22 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 8372

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4RELION5CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC43D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3831721 / Details: Particles picked with trained TOPAZ picking model
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121910 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: BamA-E / Source name: AlphaFold / Type: in silico model

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