11XY | pdb_000011xy

Escherichia coli MurJ in the outward-facing conformation

• PDB DOI: https://doi.org/10.2210/pdb11XY/pdb
• EM Map EMD-76176: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-03-17 Released: 2026-09-16 
• Deposition Author(s): Li, Y.E., Clemons, W.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), The G. Harold and Leila Y. Mathers Foundation, Chan Zuckerberg Initiative

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structures of the lipid II flippase from the monoderm pathogen Staphylococcus aureus.

Li, Y.E., Baron, G.F., Clemons Jr., W.M.

(2026) J Biol Chem : 113516-113516

• PubMed: 42700959 
• DOI: https://doi.org/10.1016/j.jbc.2026.113516
• Primary Citation Related Structures: 
  11XX, 11XY, 11XZ, 11YA


• PubMed Abstract: 
  

  Peptidoglycan biogenesis requires membrane flippases to translocate lipid-linked precursors across the cytoplasmic membrane for processing. This essential step is mediated by MurJ, the lipid II flippase conserved across all peptidoglycan-producing bacteria. While MurJ from diderm bacteria has been structurally resolved in multiple conformational states, its monoderm homolog remains uncharacterized. Monoderm MurJ homologs exhibit substantial sequence divergence yet retain the same lipid II flipping function and are promising antibiotic targets. Here we report structures of Staphylococcus aureus MurJ (SaMurJ) captured in both outward- and inward-facing conformations. These structures show that SaMurJ adopts the conserved MOP family fold and undergoes conformational transitions consistent with an alternating-access mechanism. Our findings reveal conserved and divergent features of MurJ between diderm and monoderm bacteria that are critical for lipid II flipping and provide a structural framework for probing substrate recognition and specific inhibition.

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Organizational Affiliation: 
• Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA; Chan Zuckerberg Initiative, Redwood City, California, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 55.31 kDa 
• Atom Count: 3,792 
• Modeled Residue Count: 499 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II flippase MurJ	A	511	Escherichia coli	Mutation(s): 0  Gene Names: murJ, mviN, yceN, b1069, JW1056
UniProt
Find proteins for P0AF16 (Escherichia coli (strain K12)) Explore P0AF16  Go to UniProtKB:  P0AF16

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): Li, Y.E., Clemons, W.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM114611
The G. Harold and Leila Y. Mathers Foundation	United States	--
Chan Zuckerberg Initiative	United States	--

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release