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- EMDB-71969: Cryo-EM structure of apo BAM from P. aeruginosa PAO1 -

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Basic information

Entry
Database: EMDB / ID: EMD-71969
TitleCryo-EM structure of apo BAM from P. aeruginosa PAO1
Map dataCryosparc consensus sharp map of BAM (BamA-BamE)
Sample
  • Complex: PAO1-BAM
    • Complex: BamA
      • Protein or peptide: Outer membrane protein assembly factor BamA
    • Complex: BamB
      • Protein or peptide: Outer membrane protein assembly factor BamB
    • Complex: BamC
      • Protein or peptide: Outer membrane protein assembly factor BamC
    • Complex: BamD
      • Protein or peptide: Outer membrane protein assembly factor BamD
    • Complex: BamE
      • Protein or peptide: Outer membrane protein assembly factor BamE
  • Ligand: SODIUM ION
Keywordsprotein complex / outer membrane / beta-barrel / protein folding / Gram-negative bacterial protein / MEMBRANE 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 / NlpB/DapX lipoprotein / 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 / NlpB/DapX lipoprotein / 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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / 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 (bacteria) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsMunder F / Venugopal H / Grinter R
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102150 Australia
CitationJournal: To Be Published
Title: A potent protein antibiotic kills Pseudomonas aeruginosa by inhibiting the BAM complex
Authors: Munder F / Johnson M / Samuels I / McCaughey L / Zdorevskyi O / Wang C / Kropp A / Price E / Sarovich S / Varshney S / Venugopal H / Sharma V / Doyle M / Short F / Ghosal D / Connolly J / Knott G / Grinter F
History
DepositionAug 5, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71969.png

Downloads & links

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Map

FileDownload / File: emd_71969.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryosparc consensus sharp map of BAM (BamA-BamE)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å		0.75 Å/pix.
x 320 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.84883356 - 1.1106242
Average (Standard dev.)-0.00046640373 (±0.025778363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71969_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_71969_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #3

Fileemd_71969_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined sharp map of BamA

Fileemd_71969_additional_1.map
AnnotationCryosparc local refined sharp map of BamA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined map of BamA

Fileemd_71969_additional_2.map
AnnotationCryosparc local refined map of BamA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined sharp map of BamB

Fileemd_71969_additional_3.map
AnnotationCryosparc local refined sharp map of BamB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined map of BamB

Fileemd_71969_additional_4.map
AnnotationCryosparc local refined map of BamB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined sharp map of BamDE (and C)

Fileemd_71969_additional_5.map
AnnotationCryosparc local refined sharp map of BamDE (and C)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc local refined map of BamDE (and C)

Fileemd_71969_additional_6.map
AnnotationCryosparc local refined map of BamDE (and C)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryosparc consensus map of BAM (BamA-BamE)

Fileemd_71969_additional_7.map
AnnotationCryosparc consensus map of BAM (BamA-BamE)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of consensus map

Fileemd_71969_half_map_1.map
AnnotationHalf map A of consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of consensus map

Fileemd_71969_half_map_2.map
AnnotationHalf map B of consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PAO1-BAM

EntireName: PAO1-BAM
Components
  • Complex: PAO1-BAM
    • Complex: BamA
      • Protein or peptide: Outer membrane protein assembly factor BamA
    • Complex: BamB
      • Protein or peptide: Outer membrane protein assembly factor BamB
    • Complex: BamC
      • Protein or peptide: Outer membrane protein assembly factor BamC
    • Complex: BamD
      • Protein or peptide: Outer membrane protein assembly factor BamD
    • Complex: BamE
      • Protein or peptide: Outer membrane protein assembly factor BamE
  • Ligand: SODIUM ION

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Supramolecule #1: PAO1-BAM

SupramoleculeName: PAO1-BAM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: BAM complex natively purified from P. aeruginosa PAO1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1
Molecular weightTheoretical: 19 KDa

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Supramolecule #2: BamA

SupramoleculeName: BamA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: BamA subunit of the BAM complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Supramolecule #3: BamB

SupramoleculeName: BamB / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Bamb of the BAM complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Supramolecule #4: BamC

SupramoleculeName: BamC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: BamC of the BAM complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Supramolecule #5: BamD

SupramoleculeName: BamD / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4 / Details: BamD of the BAM complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Supramolecule #6: BamE

SupramoleculeName: BamE / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5 / Details: BamE of the BAM complex
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Strain: PAO1

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Macromolecule #1: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 92.258469 KDa
SequenceString: MKRFLLPALL SALMIAEVHA ESAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGSF TVSDIRVNGL QRVSAGSVFA ALPLNVGET IDDQALVQAT RSLFKTGFFQ DIQLGRDGNV LVVTVVERPS ISSIEIEGNK AISKEDLLKG LKQSGLAEGE I FQRATLEG ...String:
MKRFLLPALL SALMIAEVHA ESAWSHPQFE KGGGSGGGSG GSAWSHPQFE KENLYFQGSF TVSDIRVNGL QRVSAGSVFA ALPLNVGET IDDQALVQAT RSLFKTGFFQ DIQLGRDGNV LVVTVVERPS ISSIEIEGNK AISKEDLLKG LKQSGLAEGE I FQRATLEG VRNELQRQYV AQGRYSAEIN AEVIPQPRNR VALKININEG TVAAISHINV VGNTVFSEED LTDLFELKTT NW LSFFKND DKYAREKLSG DLERLRSYYL DRGYINMDIA STQVSITPDK KHVYITVNIN EGEKYTIRDV KLTGDLKVPE EEV KRLLLV QKGQVFSRKV MTTTSDLITR RLGNEGYTFA NVNGVPEAHD DDKTVSVTFV VDPGKRAYVN RINFRGNTKT EDEV LRREM RQMEGGWAST YLIDQSKARL ERLGYFKEVN VETPAVPGTD DQVDVNYSVE EQPSGSITAS VGFAQSAGLI LGGSI SQNN FLGTGNKVSI GLTRSEYQTR YNFGFVDPYW TVDGVSLGYN AFYRKTDYDE LDVDVASYSV NSLGAGMSIG YPISET SRL TYGLSVQRDQ IDTGRYTVDE IYDFLDKEGD NFTNFKASIG WSESTLNKGV LATRGHSQSL TLETTLPGSD LSFYKID YR GQVFAPLTDN YTMRFHTELG YGDGYGSTER LPFYENYYAG GFNSVRGFKD STLGPRSTPS VARNPDGTPM KNQGPDSK G RYTDPDQDPE AFGGNILITG GAELLFPLPF VKDQRQLRTV LFWDVGSTFD TDCPTKTTTN CDGIKTDNLA SSVGVGLTW ITALGPLSFS LATPIKKPDN AETQVFQFSL GQTF

UniProtKB: Outer membrane protein assembly factor BamA

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Macromolecule #2: Outer membrane protein assembly factor BamB

MacromoleculeName: Outer membrane protein assembly factor BamB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 40.436656 KDa
SequenceString: MVQWKHAALL ALALAVVGCS SNSKKELPPA ELTDFKEEVV LSKQWSRSVG DGQGDLYNLL EPAVDGSTIY AASAEGRVMA IQRETGDVL WKKDLERPVS GGVGVGYGLV LVGTLRGDVI ALDEATGKKK WTKRVNSEVL SAPATNGDVV VVQTQDDKLI G LDAASGDQ ...String:
MVQWKHAALL ALALAVVGCS SNSKKELPPA ELTDFKEEVV LSKQWSRSVG DGQGDLYNLL EPAVDGSTIY AASAEGRVMA IQRETGDVL WKKDLERPVS GGVGVGYGLV LVGTLRGDVI ALDEATGKKK WTKRVNSEVL SAPATNGDVV VVQTQDDKLI G LDAASGDQ RWIYESTVPV LTLRGTGAPL IAGNMALAGL ASGKVVAVDV QRGLPIWEQR VAIPQGRSEL DRVVDIDGGL LL SGDTLYV VSYQGRAAAL DVNSGRLLWQ REASSYVGVA EGFGNIYVSQ ASGSVEGLDS RGASSLWNND ALARRQLSAP AVF SSNVVV GDLEGYVHLL SQVDGRFVGR ERVDSDGVRV RPLVVGSWMY VFGNGGKLVA YTIR

UniProtKB: Outer membrane protein assembly factor BamB

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Macromolecule #3: Outer membrane protein assembly factor BamC

MacromoleculeName: Outer membrane protein assembly factor BamC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 43.100664 KDa
SequenceString: MKRLAGLTAL ALVIGNTSGC GWLWGPEGYF RDRGDDYLGA RETPPMQLPE GVHSKPLDPL LPIPLNVATT HEKEGEYEVP RPQPLANAG DISDYSLQRS GDSRWVVAQR PPAEVWPVAR QFFEENGFRI ADERPQTGEF SSDWQSLSQL SAPLARRLSS R VSGVEPDG ...String:
MKRLAGLTAL ALVIGNTSGC GWLWGPEGYF RDRGDDYLGA RETPPMQLPE GVHSKPLDPL LPIPLNVATT HEKEGEYEVP RPQPLANAG DISDYSLQRS GDSRWVVAQR PPAEVWPVAR QFFEENGFRI ADERPQTGEF SSDWQSLSQL SAPLARRLSS R VSGVEPDG QARVRVRIEP GVQSNTSEVY VLSQTRAAGD TSSPSWPSKS VAPSLDAALL DEMVASMARS AEQGGSVSLL AA NSIYDTP GTFELSKDGS GNPVLTLQSD FDRSWVSVGR ALDNADIRVD DLNRSLGVYY VNIAEGAKKP DEDKPGFFSR LFG GGEKTK EEEDAKAQRY QVRLTTVSDA VQVTVDKDIN TSAPADVAQN VLEKLQESMR NAVRGSGQRK PGQFGLGEQF

UniProtKB: Outer membrane protein assembly factor BamC

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Macromolecule #4: Outer membrane protein assembly factor BamD

MacromoleculeName: Outer membrane protein assembly factor BamD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 38.660914 KDa
SequenceString: MQVKHLLLIA ILALTAACSS NKETVDENLS ESQLYQQAQD DLNNKSYNSA VTKLKALESR YPFGRYAEQA QLELIYANYK NMEPEAARA AAERFIRLHP QHPNVDYAYY LKGLSSFDQD RGLLARFLPL DMTKRDPGAA RDSFNEFAQL TSRFPNSRYA P DAKARMVY ...String:
MQVKHLLLIA ILALTAACSS NKETVDENLS ESQLYQQAQD DLNNKSYNSA VTKLKALESR YPFGRYAEQA QLELIYANYK NMEPEAARA AAERFIRLHP QHPNVDYAYY LKGLSSFDQD RGLLARFLPL DMTKRDPGAA RDSFNEFAQL TSRFPNSRYA P DAKARMVY LRNLLAAYEV HVGHYYLKRQ AYVAAANRGR YVVENFQETP AVGDGLAIMV EAYRRLGLDD LASTSLETLK LN YPDNASL KDGEFVARES EADTRSWLAK ATLGLIEGGE PPPHMETQAA KDVIKQYEDA EREIPAELKP ENQDHSADDE KPE SDDDED SGRSWWSYMT FGLFD

UniProtKB: Outer membrane protein assembly factor BamD

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Macromolecule #5: Outer membrane protein assembly factor BamE

MacromoleculeName: Outer membrane protein assembly factor BamE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 19.411865 KDa
SequenceString:
MQNAKLMLTC LAFAGLAALA GCSFPGVYKI DIQQGNVVTQ DMIDQLRPGM TRRQVRFIMG NPLIVDTFHA NRWDYLYSIQ PGGGRRQQE RVSLFFNDSD QLAGLNGDFM PGVSRDEAIL GKEGSTTVTQ PADQQKPEAQ KEEPPKPGST LEQLQREVDE A QPVPVPTP EPLDPSPQ

UniProtKB: Outer membrane protein assembly factor BamE

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Macromolecule #6: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 6 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

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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

Concentration2.8 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris-HCl
150.0 mMSodium chlorideNaCl

Details: Buffer originally contained 0.01 % LMNG, but before grid preparation, LMNG concentration was removed by dilution and re-concentrating in 100 kDa concentrators
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 8372 / Average exposure time: 5.22 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3831721 / Details: Particles picked with trained TOPAZ picking model
CTF correctionSoftware - Name: RELION (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 121910
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: BamA-E
Output model

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

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