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 9SOW | pdb_00009sow

BepA-BamABCDE-OMP-Nb5 complex in open, substrate-engaged beta barrel conformation.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9SOW

This is version 1.1 of the entry. See complete history. 

Literature

Stress-induced membrane insertion at the beta-barrel assembly machinery complex regulates BepA metalloprotease activity.

Voedts, H., Nguyen, P.C., Nguyen, V.S., Leverrier, P., Iorga, B.I., Cho, S.H., Remaut, H., Collet, J.F.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77559-0
  • Primary Citation Related Structures: 
    9SOW, 9SOX

  • PubMed Abstract: 

    Proteases must be tightly regulated to prevent uncontrolled degradation, yet the mechanisms ensuring such control remain poorly understood. Members of the widespread M48 metalloprotease family are kept inactive by an autoinhibitory plug that blocks catalytic water activation, but how this plug is released remained elusive. Here, using genetic, biochemical and cryo-EM approaches, we discover the activation mechanism of BepA, a quality-control protease that preserves outer membrane integrity by surveilling the β-barrel assembly machinery (BAM) in Gram-negative bacteria. Our cryo-EM analysis of BepA engaged with a stalled BAM-substrate assembly complex revealed that a flexible, unstructured α6-lid covering the active site in the latent protein functions as a molecular harpoon, inserting into the outer membrane when a substrate stalls at BAM and thereby docking BepA at the complex. This membrane anchoring promotes displacement of the autoinhibitory plug and unlocks protease activity precisely where and when it is needed. Thus, a dual enzyme activation mechanism is coupled to membrane association under stress, ensuring that BepA remains inactive until properly localized. Our findings reveal how membranes themselves can license protease activation, a principle that may extend beyond M48 metalloproteases.


  • Organizational Affiliation: 
    • WELBIO department, WEL Research Institute, avenue Pasteur 6, 1300, Wavre, Belgium.

Macromolecule Content 

  • Total Structure Weight: 265.95 kDa 
  • Atom Count: 15,079 
  • Modeled Residue Count: 1,943 
  • Deposited Residue Count: 2,418 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA810Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for C3TPJ2 (Escherichia coli)
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Go to UniProtKB:  C3TPJ2
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UniProt GroupC3TPJ2
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamB392Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P77774 (Escherichia coli (strain K12))
Explore P77774 
Go to UniProtKB:  P77774
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UniProt GroupP77774
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamC344Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12))
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UniProt GroupP0A903
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamD245Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12))
Explore P0AC02 
Go to UniProtKB:  P0AC02
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UniProt GroupP0AC02
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamE113Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12))
Explore P0A937 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-barrel assembly-enhancing proteaseF [auth H]487Escherichia coli BW25113Mutation(s): 0 
Gene Names: bepA, yfgC, b2494, JW2479
EC: 3.4
UniProt
Find proteins for P66948 (Escherichia coli (strain K12))
Explore P66948 
Go to UniProtKB:  P66948
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UniProt GroupP66948
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown beta-barrel substrateG [auth P]27Escherichia coli BW25113Mutation(s): 0 
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)BelgiumG0G0818N
Research Foundation - Flanders (FWO)Belgium12ZM421N

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-10-21
    Changes: Data collection, Database references