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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23664 | |||||||||
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Title | Multidrug Efflux pump AdeJ | |||||||||
![]() | Multidrug Efflux pump AdeJ | |||||||||
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![]() | multidrug efflux pump / MEMBRANE PROTEIN | |||||||||
Function / homology | Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / plasma membrane / Efflux pump membrane transporter![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
![]() | Zhang Z | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM Determination of Eravacycline-Bound Structures of the Ribosome and the Multidrug Efflux Pump AdeJ of Acinetobacter baumannii. Authors: Zhemin Zhang / Christopher E Morgan / Robert A Bonomo / Edward W Yu / ![]() Abstract: Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections ...Antibiotic-resistant strains of the Gram-negative pathogen Acinetobacter baumannii have emerged as a significant global health threat. One successful therapeutic option to treat bacterial infections has been to target the bacterial ribosome. However, in many cases, multidrug efflux pumps within the bacterium recognize and extrude these clinically important antibiotics designed to inhibit the protein synthesis function of the bacterial ribosome. Thus, multidrug efflux within A. baumannii and other highly drug-resistant strains is a major cause of failure of drug-based treatments of infectious diseases. We here report the first structures of the cinetobacter rug fflux (Ade)J pump in the presence of the antibiotic eravacycline, using single-particle cryo-electron microscopy (cryo-EM). We also describe cryo-EM structures of the eravacycline-bound forms of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. Our data indicate that the AdeJ pump primarily uses hydrophobic interactions to bind eravacycline, while the 70S ribosome utilizes electrostatic interactions to bind this drug. Our work here highlights how an antibiotic can bind multiple bacterial targets through different mechanisms and potentially enables drug optimization by taking advantage of these different modes of ligand binding. Acinetobacter baumannii has developed into a highly antibiotic-resistant Gram-negative pathogen. The prevalent AdeJ multidrug efflux pump mediates resistance to different classes of antibiotics known to inhibit the function of the 70S ribosome. Here, we report the first structures of the A. baumannii AdeJ pump, both in the absence and presence of eravacycline. We also describe structures of the A. baumannii ribosome bound by this antibiotic. Our results indicate that AdeJ and the ribosome use very distinct binding modes for drug recognition. Our work will ultimately enable structure-based drug discovery to combat antibiotic-resistant A. baumannii infection. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 9.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.8 KB 9.8 KB | Display Display | ![]() |
Images | ![]() | 170.3 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m4qMC ![]() 7m4pC ![]() 7m4uC ![]() 7m4vC ![]() 7m4wC ![]() 7m4xC ![]() 7m4yC ![]() 7m4zC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Multidrug Efflux pump AdeJ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : multidrug efflux pump AdeJ
Entire | Name: multidrug efflux pump AdeJ |
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Components |
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-Supramolecule #1: multidrug efflux pump AdeJ
Supramolecule | Name: multidrug efflux pump AdeJ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Efflux pump membrane transporter
Macromolecule | Name: Efflux pump membrane transporter / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 114.637781 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAQFFIHRPI FAWVIALVIM LAGILTLTKM PIAQYPTIAP PTVTIAATYP GASAETVENT VTQIIEQQMN GLDGLRYISS NSAGNGQAS IQLNFEQGVD PDIAQVQVQN KLQSATALLP EDVQRQGVTV TKSGASFLQV IAFYSPDNNL SDSDIKDYVN S SIKEPLSR ...String: MAQFFIHRPI FAWVIALVIM LAGILTLTKM PIAQYPTIAP PTVTIAATYP GASAETVENT VTQIIEQQMN GLDGLRYISS NSAGNGQAS IQLNFEQGVD PDIAQVQVQN KLQSATALLP EDVQRQGVTV TKSGASFLQV IAFYSPDNNL SDSDIKDYVN S SIKEPLSR VAGVGEVQVF GGSYAMRIWL DPAKLTSYQL TPSDIATALQ AQNSQVAVGQ LGGAPAVQGQ VLNATVNAQS LL QTPEQFK NIFLKNTASG AEVRLKDVAR VELGSDNYQF DSKFNGKPAA GLAIKIATGA NALDTAEAVE QRLSELRKNY PTG LADKLA YDTTPFIRLS IESVVHTLIE AVILVFIVMF LFLQNWRATI IPTLAVPVVV LGTFAVINIF GFSINTLTMF AMVL AIGLL VDDAIVVVEN VERVMSEDHT DPVTATSRSM QQISGALVGI TSVLTAVFVP MAFFGGTTGV IYRQFSITLV TAMVL SLIV ALTFTPALCA TILKQHDPNK EPSNNIFARF FRSFNNGFDR MSHSYQNGVS RMLKGKIFSG VLYAVVVALL VFLFQK LPS SFLPEEDQGV VMTLVQLPPN ATLDRTGKVI DTMTNFFMNE KDTVESIFTV SGFSFTGVGQ NAGIGFVKLK DWSKRTT PE TQIGSLIQRG MALNMIIKDA SYVMPLQLPA MPELGVTAGF NLQLKDSSGQ GHEKLIAARN TILGLASQDK RLVGVRPN G QEDTPQYQIN VDQAQAGAMG VSIAEINNTM RIAWGGSYIN DFVDRGRVKK VYVQGDAGSR MMPEDLNKWY VRNNKGEMV PFSAFATGEW TYGSPRLERY NGVSSVNIQG TPAPGVSSGD AMKAMEEIIG KLPSMGLQGF DYEWTGLSLE ERESGAQAPF LYALSLLIV FLCLAALYES WSIPFSVLLV VPLGVIGAIV LTYLGMIIKG DPNLSNNIYF QVAIIAVIGL SAKNAILIVE F AKELQEKG EDLLDATLHA AKMRLRPIIM TTLAFGFGVL PLALSTGAGA GSQHSVGFGV LGGVLSATFL GIFFIPVFYV WI RSIFKYK PKTINTQEHK S UniProtKB: Efflux pump membrane transporter |
-Macromolecule #2: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 2 / Number of copies: 8 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ![]() ChemComp-3PE: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83768 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |