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- PDB-20yy: Cryo-EM structure of MexJK from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 20yy
TitleCryo-EM structure of MexJK from Pseudomonas aeruginosa
Components
  • Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
  • Multidrug efflux RND transporter permease subunit MexK
KeywordsTRANSPORT PROTEIN / HAE1-RND family efflux pump
Function / homologyTRICLOSAN / : / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsWu, Z.K. / Long, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2026
Title: Structural insights into a substrate translocation pathway revealed by the RND efflux pump complex MexJK from Pseudomonas aeruginosa
Authors: Wu, Z.K. / Long, F.
History
DepositionDec 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Multidrug efflux RND transporter permease subunit MexK
B: Multidrug efflux RND transporter permease subunit MexK
C: Multidrug efflux RND transporter permease subunit MexK
D: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
E: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
F: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
G: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
H: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
I: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)568,70212
Polymers567,8349
Non-polymers8693
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 Multidrug efflux RND transporter permease subunit MexK / Resistance-nodulation-cell division (RND) efflux transporter


Mass: 113392.469 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexK, CAZ10_17050, GUL26_01775 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2C9WXC2
#2: Protein
Multidrug efflux RND transporter periplasmic adaptor subunit MexJ


Mass: 37942.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: mexJ, F7R07_07310 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A643ENN9
#3: Chemical ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic, detergent*YM
Has ligand of interestY
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: Structure of MexJK / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 573 kDa/nm / Experimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20mM Hepes,150mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
220 mM4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acidHepes1
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Details: Microscope model is FEI TITAN KRIOS,I can not find this model in the given list
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.2_4158model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240140 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.57 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00228611
ELECTRON MICROSCOPYf_angle_d0.50538886
ELECTRON MICROSCOPYf_dihedral_angle_d4.0393981
ELECTRON MICROSCOPYf_chiral_restr0.0414521
ELECTRON MICROSCOPYf_plane_restr0.0044992

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