9G3D | pdb_00009g3d

Cryo-EM structure of SbmA in the inward-facing-narrow conformation bound to 2 sybodies

• PDB DOI: https://doi.org/10.2210/pdb9G3D/pdb
• EM Map EMD-50994: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli MC1061
• Mutation(s): No 


• Deposited: 2024-07-12 Released: 2025-07-23 
• Deposition Author(s): Thangaratnarajah, C., Ettema, T.W., Slotboom, D.J.
• Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), European Union (EU)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of the SbmA in the inward-facing closed conformation bound to 2 sybodies

Thangaratnarajah, C., Ettema, T.W., Slotboom, D.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 131.33 kDa 
• Atom Count: 8,210 
• Modeled Residue Count: 1,010 
• Deposited Residue Count: 1,144 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide antibiotic transporter SbmA	A, B	426	Escherichia coli	Mutation(s): 0  Gene Names: sbmA, b0377, JW0368
UniProt
Find proteins for P0AFY6 (Escherichia coli (strain K12)) Explore P0AFY6  Go to UniProtKB:  P0AFY6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sybody 2	C, D	146	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGT (Subject of Investigation/LOI)	E [auth A], F [auth B]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C40 H79 O10 P KBPVYRBBONZJHF-AMAPPZPBSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.24 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.20.1-4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Thangaratnarajah, C., Ettema, T.W., Slotboom, D.J.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	714.018.003
Netherlands Organisation for Scientific Research (NWO)	Netherlands	024.003.019
Netherlands Organisation for Scientific Research (NWO)	Netherlands	184.034.014
European Union (EU)	European Union	847675

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release