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- PDB-9pxj: Cryo-EM structure of BAM from P. aeruginosa P28 in complex with P... -

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Basic information

Entry
Database: PDB / ID: 9pxj
TitleCryo-EM structure of BAM from P. aeruginosa P28 in complex with Pyocin L2
Components
  • BamA
  • Pyocin L2
KeywordsMEMBRANE PROTEIN / protein complex / outer membrane / beta-barrel / protein folding / Gram-negative bacterial protein / L-type bacteriocin / pyocin
Biological speciesPseudomonas aeruginosa (bacteria)
Pseudomonas aeruginosa 62 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsMunder, F. / 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
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BamA
F: Pyocin L2


Theoretical massNumber of molelcules
Total (without water)116,5652
Polymers116,5652
Non-polymers00
Water00
1


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

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Components

#1: Protein BamA


Mass: 88129.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: P28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Protein Pyocin L2


Mass: 28436.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 62 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
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

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1P28-BAM-PyocinL2COMPLEXP28-BamA in the background of PAO1 BamB-E in complex with Pyocin L2all0RECOMBINANT
2BamACOMPLEX#11RECOMBINANT
3Pyocin L2COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.257 MDaNO
210.086 MDaNO
310.028 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Pseudomonas aeruginosa (bacteria)287
32Pseudomonas aeruginosa (bacteria)287P28
43Pseudomonas aeruginosa (bacteria)28762
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Escherichia coli (E. coli)562C41(DE3)
32Escherichia coli (E. coli)562C41(DE3)
43Escherichia coli (E. coli)562C41(DE3)
Buffer solutionpH: 8
Details: LMNG detergent was removed by diluting the sample and re-concentrating in a 100 kDa cut-off concentrator
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris-HCl1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid 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: 277.15 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: 96000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7.6 sec. / Electron dose: 53 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11319

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2EPUimage acquisition
4RELION5CTF correction
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.6initial Euler assignment
10cryoSPARC4.6final Euler assignment
12cryoSPARC4.63D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5533458 / Details: particles picked with TOPAZ trained model
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126889 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDChain-IDSource nameType
11AAlphaFoldin silico model
21FAlphaFoldin silico model

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