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- PDB-22xm: MexBYB-Ka symmetry-like -

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Basic information

Entry
Database: PDB / ID: 22xm
TitleMexBYB-Ka symmetry-like
ComponentsMexBYB
KeywordsMEMBRANE PROTEIN / RND / Chimera / Multidrug Efflux Pump
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsWang, J. / Nakagawa, A. / Yamashita, E.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJSP2138 Japan
Japan Society for the Promotion of Science (JSPS)21K19337 Japan
Japan Society for the Promotion of Science (JSPS)23K23822 Japan
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2026
Title: Cryo-EM structures of a MexB-MexY chimeric efflux pump reveal that large open clefts are intrinsic to the MexY porter domain.
Authors: Jiye Wang / Kenta Tsutsumi / Mika Hirose / Ryosuke Nakashima / Takayuki Kato / Kunihiko Nishino / Atsushi Nakagawa / Eiki Yamashita /
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. ...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.
History
DepositionJan 27, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MexBYB
C: MexBYB
A: MexBYB


Theoretical massNumber of molelcules
Total (without water)340,5623
Polymers340,5623
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MexBYB


Mass: 113520.539 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MexB-MexY chimera protein / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Buffer solution
IDSpecimen-IDpHDetails
116.5150 mM NaCl, 10mM Kanamycin
226.510mM Kanamycin
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMSodium hydrogen phosphateNa2HPO41
220 mMSodium dihydrogen phosphateNaH2PO41
320 mMSodium hydrogen phosphateNa2HPO42
420 mMSodium dihydrogen phosphateNaH2PO42
Specimen
IDConc. (mg/ml)Experiment-IDEmbedding appliedShadowing appliedStaining appliedVitrification applied
11.81NONONOYES
22.21NONONOYES
Specimen support
IDSpecimen-IDGrid materialGrid mesh size (divisions/in.)Grid type
11COPPER300Quantifoil R1.2/1.3
22COPPER300Quantifoil R1.2/1.3
Vitrification
IDInstrumentCryogen nameHumidity (%)Specimen-IDChamber temperature (K)Entry-ID
1FEI VITROBOT MARK IVETHANE88127722XM
2FEI VITROBOT MARK IVETHANE100227722XM

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm

IDSpecimen-ID
11
22
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150FEI FALCON III (4k x 4k)
2250FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2PHENIX1.20.1_4487model refinement
15cryoSPARC4.7.03D reconstruction
Image processingDetails: We mixed data (1) and (2) to reconstruct.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 163530 / Symmetry type: POINT
RefinementHighest resolution: 3.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00323127
ELECTRON MICROSCOPYf_angle_d0.64831391
ELECTRON MICROSCOPYf_dihedral_angle_d4.2613210
ELECTRON MICROSCOPYf_chiral_restr0.0413623
ELECTRON MICROSCOPYf_plane_restr0.0054022

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