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- PDB-9sox: BepA-BamABCDE-Nb32 complex in inward open conformation with later... -

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Basic information

Entry
Database: PDB / ID: 9sox
TitleBepA-BamABCDE-Nb32 complex in inward open conformation with lateral seam closed
Components
  • (Outer membrane protein assembly factor ...) x 5
  • Beta-barrel assembly-enhancing protease
KeywordsMEMBRANE PROTEIN / M48 metalloprotease family / outer membrane protein / beta-barrel assembly machinery / cell envelope / BepA / BAM
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / Secretion of toxins / protein insertion into membrane / : / cell outer membrane / metalloendopeptidase activity / outer membrane-bounded periplasmic space ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / Secretion of toxins / protein insertion into membrane / : / cell outer membrane / metalloendopeptidase activity / outer membrane-bounded periplasmic space / protein-macromolecule adaptor activity / response to antibiotic / cell surface / metal ion binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Beta-barrel assembly-enhancing protease / : / Peptidase M48 / Peptidase family M48 / Outer membrane protein assembly factor BamC / 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 ...Beta-barrel assembly-enhancing protease / : / Peptidase M48 / Peptidase family M48 / Outer membrane protein assembly factor BamC / 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 / Tetratricopeptide repeat / Pyrrolo-quinoline quinone repeat / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 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 BamA / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamD / Beta-barrel assembly-enhancing protease / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.4 Å
AuthorsNguyen, V.S. / Remaut, H. / Nguyen, P.C. / Voedts, H. / Collet, J.F.
Funding support Belgium, 3items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G0G0818N Belgium
Research Foundation - Flanders (FWO)12ZM421N Belgium
CitationJournal: Nat Commun / Year: 2026
Title: Stress-induced membrane insertion at the beta-barrel assembly machinery complex regulates BepA metalloprotease activity
Authors: Voedts, H. / Nguyen, P.C. / Nguyen, V.S. / Leverrier, P. / Iorga, B.I. / Cho, S.H. / Remaut, H. / Collet, J.F.
History
DepositionSep 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
H: Beta-barrel assembly-enhancing protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,6357
Polymers263,5706
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: 90643.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: C3TPJ2
#2: Protein Outer membrane protein assembly factor BamB


Mass: 41918.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P77774
#3: Protein Outer membrane protein assembly factor BamC


Mass: 36875.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A903
#4: Protein Outer membrane protein assembly factor BamD


Mass: 27858.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0AC02
#5: Protein Outer membrane protein assembly factor BamE


Mass: 12310.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BW25113 (bacteria) / References: UniProt: P0A937

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Protein / Non-polymers , 2 types, 2 molecules H

#6: Protein Beta-barrel assembly-enhancing protease


Mass: 53962.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: bepA, yfgC, b2494, JW2479 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P66948, Hydrolases; Acting on peptide bonds (peptidases)
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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

ComponentName: BepA-BamABCDE complex with nanobody32 / Type: COMPLEX
Details: The complex was purified from over-expression of a BepA inactive mutant in E. coli K12. BepA has a twinstrep tag at the C-terminal. The complex was first pulled on twinstrep tag using Strep- ...Details: The complex was purified from over-expression of a BepA inactive mutant in E. coli K12. BepA has a twinstrep tag at the C-terminal. The complex was first pulled on twinstrep tag using Strep-TactinXT 4Flow high capacity resin, then mixed with BamA nanobody32-his and pulled on his tag using Ni-NTA resin.
Entity ID: #1-#6 / Source: RECOMBINANT
Molecular weightValue: 0.26 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Source (recombinant)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMtrisaminomethaneC4H11NO31
2150 mMSodium ChlorideNaCl1
3300 mMImidazoleC3H2N41
40.03 %n-dodecyl-beta-D-maltosideC24H46O111
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: 2-side blotting for 5 seconds

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10904

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Processing

EM software
IDNameVersionCategory
1SPHIREparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3449013
3D reconstructionResolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24620 / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE

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