9G4E | pdb_00009g4e

CryoEM structure of the proton-dependent antibacterial peptide transporter SbmA in complex with FabS11-1 in lipid nanodiscs at pH 5.5, inward-open state

• PDB DOI: https://doi.org/10.2210/pdb9G4E/pdb
• EM Map EMD-51036: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus, Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-07-15 Released: 2025-07-30 
• Deposition Author(s): Ghilarov, D., Beis, K.
• Funding Organization(s): Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC), European Regional Development Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and mechanism of SLiPT transporters

Ettema, T.W., Thangaratnarajah, C., Inaba-Inoue, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 141.24 kDa 
• Atom Count: 9,660 
• Modeled Residue Count: 1,215 
• Deposited Residue Count: 1,258 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
11-1 FabH	A [auth C]	233	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
11-1 FabL	B [auth D]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide antibiotic transporter SbmA	C [auth A], D [auth B]	406	Escherichia coli	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0AFY6 (Escherichia coli (strain K12)) Explore P0AFY6  Go to UniProtKB:  P0AFY6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 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: 2025-07-30 
Deposition Author(s): Ghilarov, D., Beis, K.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221868/Z/20/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/X01097X/1
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/H01778X/1
European Regional Development Fund	European Union	TEAM/2016-3/23

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release