9HE1 | pdb_00009he1

Structure of the Xenorceptide A2-bound E. coli BAM complex (BamABCDE)

• PDB DOI: https://doi.org/10.2210/pdb9HE1/pdb
• EM Map EMD-52074: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTM


• Deposited: 2024-11-13 Released: 2025-02-26 
• Deposition Author(s): Jakob, R.P., Modaresi, S.M., Maier, T., Hiller, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA

Modaresi, S.M., Sugiyama, R., Tram, N.D.T., Jakob, R.P., Phan, C.S., Saei, A.A., Morishita, Y., Muhlethaler, T., Lim, J., Ritz, D., Long, P.S.Y., Lehner, P.A., Lim, Z.H., Degen, M., Yao, Z., Maier, T., Hou, Y., Lee, J.Y., Xu, J., Yeat, A.Y.J., Koh, K.T.S., Goh, W.Y., Ling, S.Y.H., Chua, P.W.L., Yamazaki, M., Ee, P.L.R., Hiller, S., Morinaka, B.I.

(2024) bioRxiv 

• DOI: https://doi.org/10.1101/2024.12.16.628070

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 213.22 kDa 
• Atom Count: 11,837 
• Modeled Residue Count: 1,511 
• Deposited Residue Count: 1,932 
• 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 K-12	Mutation(s): 0  Gene Names: bamA, yaeT, yzzN, yzzY, b0177, JW0172 Membrane Entity: Yes
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12)) Explore P0A940  Go to UniProtKB:  P0A940

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamB	B	400	Escherichia coli K-12	Mutation(s): 0  Gene Names: bamB, yfgL, b2512, JW2496 Membrane Entity: Yes
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 K-12	Mutation(s): 0  Gene Names: bamC, dapX, nlpB, b2477, JW2462 Membrane Entity: Yes
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 K-12	Mutation(s): 0  Gene Names: bamD, yfiO, b2595, JW2577 Membrane Entity: Yes
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	121	Escherichia coli K-12	Mutation(s): 0  Gene Names: bamE, smpA, b2617, JW2598 Membrane Entity: Yes
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
RSAM-modified RiPP, XyeA family	F [auth G]	12	synthetic construct	Mutation(s): 0
UniProt
Find proteins for A0A1Q4P361 (Serratia marcescens) Explore A0A1Q4P361  Go to UniProtKB:  A0A1Q4P361

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Jakob, R.P., Modaresi, S.M., Maier, T., Hiller, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release