22XM | pdb_000022xm

MexBYB-Ka symmetry-like

• PDB DOI: https://doi.org/10.2210/pdb22XM/pdb
• EM Map EMD-67813: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Mutation(s): No 


• Deposited: 2026-01-27 Released: 2026-03-11 
• Deposition Author(s): Wang, J., Nakagawa, A., Yamashita, E.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of a MexB-MexY chimeric efflux pump reveal that large open clefts are intrinsic to the MexY porter domain.

Wang, J., Tsutsumi, K., Hirose, M., Nakashima, R., Kato, T., Nishino, K., Nakagawa, A., Yamashita, E.

(2026) Acta Crystallogr F Struct Biol Commun 

• PubMed: 41744473 
• DOI: https://doi.org/10.1107/S2053230X26001202
• Primary Citation of Related Structures:  
  22XK, 22XM


• PubMed Abstract: 
  

  RND-type multidrug-efflux pumps are major contributors to multidrug resistance in Gram-negative bacteria, with MexY from Pseudomonas aeruginosa playing a central role in aminoglycoside resistance. Unlike other RND transporters, MexY exhibits unusually large open clefts in the binding and extrusion states. To determine whether this feature is intrinsic to its drug-recognition porter domain, we created a chimeric protein, MexBYB, by replacing the funnel-like and transmembrane domains of MexY with those of the homologous transporter MexB, and determined its structures by cryoEM under apo and kanamycin-supplemented conditions. Under both conditions, MexBYB was reported to adopt symmetric-like and asymmetric conformations. Structural comparisons reveal that the unusually large open clefts are retained in MexBYB, indicating that this feature is intrinsic to the MexY porter domain.

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Organizational Affiliation: 
• Laboratory for Supramolecular Crystallography, Institute for Protein Research, The University of Osaka, Suita, Osaka 565-0871, Japan.
Laboratory for High Resolution Cryo-EM, Institute for Protein Research, The University of Osaka, Suita, Osaka 565-0871, Japan.
Biomolecular Science and Regulation Department, SANKEN, The University of Osaka, Ibaraki, Osaka 567-0047, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 340.56 kDa 
• Atom Count: 22,677 
• Modeled Residue Count: 2,975 
• Deposited Residue Count: 3,147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MexBYB	A [auth B], B [auth C], C [auth A]	1,049	Pseudomonas aeruginosa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-11 
Deposition Author(s): Wang, J., Nakagawa, A., Yamashita, E.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJSP2138
Japan Society for the Promotion of Science (JSPS)	Japan	21K19337
Japan Society for the Promotion of Science (JSPS)	Japan	23K23822

Revision History  

• Version 1.0: 2026-03-11
  Type: Initial release