9SOX | pdb_00009sox

BepA-BamABCDE-Nb32 complex in inward open conformation with lateral seam closed

• PDB DOI: https://doi.org/10.2210/pdb9SOX/pdb
• EM Map EMD-55064: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli BW25113
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2025-09-16 Released: 2026-09-30 
• Deposition Author(s): Nguyen, V.S., Remaut, H., Nguyen, P.C., Voedts, H., Collet, J.F.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 

• DOI: https://doi.org/10.1038/s41467-026-77559-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 263.64 kDa 
• Atom Count: 16,344 
• Modeled Residue Count: 2,092 
• Deposited Residue Count: 2,391 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A	810	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for C3TPJ2 (Escherichia coli) Explore C3TPJ2  Go to UniProtKB:  C3TPJ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamB	B	392	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P77774 (Escherichia coli (strain K12)) Explore P77774  Go to UniProtKB:  P77774

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamC	C	344	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A903 (Escherichia coli (strain K12)) Explore P0A903  Go to UniProtKB:  P0A903

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamD	D	245	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0AC02 (Escherichia coli (strain K12)) Explore P0AC02  Go to UniProtKB:  P0AC02

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamE	E	113	Escherichia coli BW25113	Mutation(s): 0
UniProt
Find proteins for P0A937 (Escherichia coli (strain K12)) Explore P0A937  Go to UniProtKB:  P0A937

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-barrel assembly-enhancing protease	F [auth H]	487	Escherichia coli BW25113	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-30 
Deposition Author(s): Nguyen, V.S., Remaut, H., Nguyen, P.C., Voedts, H., Collet, J.F.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0H5916N
Research Foundation - Flanders (FWO)	Belgium	G0G0818N
Research Foundation - Flanders (FWO)	Belgium	12ZM421N

Revision History  

• Version 1.0: 2026-09-30
  Type: Initial release