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- EMDB-67813: MexBYB-Ka symmetry-like -

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Basic information

Entry
Database: EMDB / ID: EMD-67813
TitleMexBYB-Ka symmetry-like
Map data
Sample
  • Complex: MexB-MexY chimera protein
    • Protein or peptide: MexBYB
KeywordsRND / Chimera / Multidrug Efflux Pump / MEMBRANE PROTEIN
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsWang J / Nakagawa A / Yamashita E
Funding support Japan, 3 items
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
DepositionDec 18, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67813.png

Downloads & links

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Map

FileDownload / File: emd_67813.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 Å		1.35 Å/pix.
x 256 pix.
= 345.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3491692 - 0.850618
Average (Standard dev.)0.000269526 (±0.017823603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_67813_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_67813_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_67813_half_map_2.map
Projections & Slices
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Sample components

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Entire : MexB-MexY chimera protein

EntireName: MexB-MexY chimera protein
Components
  • Complex: MexB-MexY chimera protein
    • Protein or peptide: MexBYB

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Supramolecule #1: MexB-MexY chimera protein

SupramoleculeName: MexB-MexY chimera protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 113 KDa

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Macromolecule #1: MexBYB

MacromoleculeName: MexBYB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MSKFFIDRPI FAWVIALVIM LAGGLSILFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASLT LTFRQGVNAD LAAVEVQNRL KIVESRLPES VRRDGIYVEK AADSIQLIVT LTSSSGRYDA MELGEIASSN VLQALRRVEG ...String:
MSKFFIDRPI FAWVIALVIM LAGGLSILFL PVAQYPDIAP PVVNVSASYP GASAKVVEEA VTAIIEREMN GAPGLLYTKA TSSTGQASLT LTFRQGVNAD LAAVEVQNRL KIVESRLPES VRRDGIYVEK AADSIQLIVT LTSSSGRYDA MELGEIASSN VLQALRRVEG VGKVETWGAE YSMRIWLDPA KLNSYQLTPG DVSSAIQAQN VQISSGQLGG LPAVKGQQLN ATIIGKTRLQ TAEQFENILL KVNPDGSQVR LKDVADVGLG GQDYGFVSRV NQMTATGLAV KMAPGSNAVA TAKRIRATLD ELSRYFPEGV SYNIPYDTSA FVEISIRKVV KTLGEAILLV FLVMYLFLQN FRATLIPTIA VPVVLLGTFG VLAAFGFSIN TLTMFGMVLA IGLLVDDAIV VVENVERVMA EEGLSPREAA RKSMGQIQGA LVGIAMVLSA VFLPMAFFGG STGVIYRQFS ITIVSAMALS VIVALILTPA LCATMLKPIE KGDHGEHKGG FFGWFNRMFL STTHGYERGV ASILKHRAPY LLIYVVIVAG MIWMFTRLPQ AFLPEEDQGD FMIMVMQPEG SSAERTMANV GDVERYLAEH EPVAYAYAVG GFSLYGDGTS SAMIFATLKD WSERREASQH VGAIVERINQ RFAGLPNRTV YAMNSPPLPD LGSTSGFDFR LQDRGGVGYE ALVKARDQLL ARAAEDPRLA NVMFAGQGEA PQYKLEIDDE KASALGVSLA DINSTVSIAW GSSYVNDFID RGRVKRVYLQ GRPDARMNPD DLSKWYVRND KGEMVPFNAF ATGKWEYGPP QLTRYNGYPS FNLEGQAAPG YSSGEAMQAM EQLMQGLPEG IAHEWSGQSF EERLSGAQAP ALYALSLLVV FLCLAALYES WSIPFSVMLV VPLGVIGALL ATSMRGLSND VFFQVGLLTT IGLSAKNAIL IVEFAKELHE QGKGIVEAAI EACRMRLRPI VMTSLAFILG VVPLAISTGA GSGSQHAIGT GVIGGMVTAT VLAIFWVPLF YVAVSTLFKD EASKQQASVE KGQHHHHHH

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
Concentration1.8 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMNa2HPO4Sodium hydrogen phosphate
20.0 mMNaH2PO4Sodium dihydrogen phosphate

Details: NaCl 150mM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Sample preparation #2

Preparation ID2
Concentration2.2 mg/mL
BufferpH: 6.5
Component:
ConcentrationFormulaName
20.0 mMNa2HPO4Sodium hydrogen phosphate
20.0 mMNaH2PO4Sodium dihydrogen phosphate

Details: NaCl 150mM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 88 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy #1

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 1 / Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeTFS KRIOS
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
DetailsWe mixed data (1) and (2) to reconstruct
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 163530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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