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- EMDB-67423: Cryo-EM structure of MexJK from Pseudomonas aeruginosa -

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Basic information

Entry
Database: EMDB / ID: EMD-67423
TitleCryo-EM structure of MexJK from Pseudomonas aeruginosa
Map data
Sample
  • Complex: Structure of MexJK
    • Protein or peptide: Multidrug efflux RND transporter permease subunit MexK
    • Protein or peptide: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
  • Ligand: TRICLOSAN
KeywordsHAE1-RND family efflux pump / TRANSPORT PROTEIN
Function / homology: / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsWu ZK / Long F
Funding support China, 1 items
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 ZK / Long F
History
DepositionDec 3, 2025-
Header (metadata) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67423.png

Downloads & links

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Map

FileDownload / File: emd_67423.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.23971362 - 0.5567452
Average (Standard dev.)0.002707808 (±0.018915448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of MexJK

EntireName: Structure of MexJK
Components
  • Complex: Structure of MexJK
    • Protein or peptide: Multidrug efflux RND transporter permease subunit MexK
    • Protein or peptide: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
  • Ligand: TRICLOSAN

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Supramolecule #1: Structure of MexJK

SupramoleculeName: Structure of MexJK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 573 kDa/nm

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Macromolecule #1: Multidrug efflux RND transporter permease subunit MexK

MacromoleculeName: Multidrug efflux RND transporter permease subunit MexK
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 113.392469 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFNLSAWAL QNRQIVLYLM ILLGAVGALS YSKLGQSEDP PFTFKAMVVQ TNWPGASAEE VARQVTERIE KKLMETGDYD RIVSFSRPG VSQVTFMARE DIHSSEIPEL WYQIRKKISD IRATLPQSIQ GPFFNDEFGT TYGNIYALTG KGFDYAVMKD Y ADRLQLQL ...String:
MSFNLSAWAL QNRQIVLYLM ILLGAVGALS YSKLGQSEDP PFTFKAMVVQ TNWPGASAEE VARQVTERIE KKLMETGDYD RIVSFSRPG VSQVTFMARE DIHSSEIPEL WYQIRKKISD IRATLPQSIQ GPFFNDEFGT TYGNIYALTG KGFDYAVMKD Y ADRLQLQL QRIRNVGKVE LIGLQDEKIW IDLSNTKLAT LGLPLAAVQK ALEEQNAVAS SGFFETASDR VQLRVSGRFD SV EEIRDFP IRVGDRTFRI GDVAEVRRGF NDPPAPRMRF MGEDAIGLAV AMKPGGDILV LGKALETEFA RLQQSLPAGL ELR KVSDQP AAVRTGVGEF IRVLAEALVI VLLVSFFSLG LRTGLVVALS IPLVLAMTFA AMHYFGIGLH KISLGALVLA LGLL VDDAI IAVEMMAVKM EQGYDRLKAA SFAWTSTAFP MLTGTLITAA GFLPIATAQS GTGEYTRSLF QVVTIALVVS WFAAV VFVP YLGAKLLPDL ARLHAQKHGG SADGYDPYAT AFYQRFRRLV EWCVRYRKTV IVLTLAAFVG ALLLFRLVPQ QFFPPS ARL ELLLDIKLAE GASLRSTGEE VQRLEKMLQG HDGIDNYVAY VGTGSPRFYL PLDQQLPAAS FAQVVVLAKD LESREAL RK WLIERMNEDF PHLRSRISRL ENGPPVGYPV QFRVSGEDIP QVRELARKVA DKMRENPHVV NVHLDWEEPS KVVYLSID Q ERARALGVST ASLSQFLQSA LTGSHVSFFR EDNELIEILL RGTEQERRDL SLLPSLAVPT ENGRSVALSQ IATLEYGFE EGIIWHRNRL PTVTVRADIY DDSLPATLVA QIAPTLEPIR AELPDGYLLE VGGTVEDAAK GQSSVNAGVP LFIVVVLSLL MVQLRSFSR MAMVFLTAPL GLIGVTLFLL LFRQPFGFVA MLGTIALAGM IMRNSVILVD QIEQDISHGL DRWHAIIEAT V RRFRPIVL TALAAVLAMI PLSRSVFFGP MAVAIMGGLI VATVLTLLFL PALYAAWFRV KKDEARA

UniProtKB: UNIPROTKB: A0A2C9WXC2

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Macromolecule #2: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ

MacromoleculeName: Multidrug efflux RND transporter periplasmic adaptor subunit MexJ
type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.942711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CGNGTPPPAA ARPAIVVQPQ PAGEVSQAFP GEIRARHEPE LAFRIGGKVI RRLVEVGERV KKDQPLAELD PQDVRLQLEA ARAQVSAAE ANLQTVRAEY RRYRTLLDRN LVSHSQFENI QNSYRAGEAR LKQIRAEFNV ADNQAGYAVL RSPQDGVIAS R RVEVGQVV ...String:
CGNGTPPPAA ARPAIVVQPQ PAGEVSQAFP GEIRARHEPE LAFRIGGKVI RRLVEVGERV KKDQPLAELD PQDVRLQLEA ARAQVSAAE ANLQTVRAEY RRYRTLLDRN LVSHSQFENI QNSYRAGEAR LKQIRAEFNV ADNQAGYAVL RSPQDGVIAS R RVEVGQVV AAGQTVFSLA ADGEREVLIG LPEHSFERFR IGQPVSVELW SQRDRRFAGH IRELSPAADP QSRTFAARVA FD DRATPAE LGQSARVYVA AAEAVPLSVP LSALTAEAGQ AFVWVVEPGS STLRRQAVRT GPYAEDRVPV LEGLKAGDWV VAT GVQVLR EGQQVRPIDR ANRTVKLAAK E

UniProtKB: UNIPROTKB: A0A643ENN9

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Macromolecule #3: TRICLOSAN

MacromoleculeName: TRICLOSAN / type: ligand / ID: 3 / Number of copies: 3 / Formula: TCL
Molecular weightTheoretical: 289.542 Da
Chemical component information

ChemComp-TCL:
TRICLOSAN / antifungal, antibiotic, detergent*YM

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMHepes4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid

Details: 20mM Hepes,150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
DetailsMicroscope model is FEI TITAN KRIOS,I can not find this model in the given list
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 240140
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

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

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