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- PDB-7b8q: Acinetobacter baumannii multidrug transporter AdeB in L*OO state -

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Entry
Database: PDB / ID: 7b8q
TitleAcinetobacter baumannii multidrug transporter AdeB in L*OO state
ComponentsEfflux pump membrane transporter
KeywordsTRANSPORT PROTEIN / RND-transporter / multidrug transporter / antibiotic resistance / membrane protein
Function / homologyHydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family / xenobiotic transport / efflux transmembrane transporter activity / response to toxic substance / plasma membrane / Efflux pump membrane transporter
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsOrnik-Cha, A. / Reitz, J. / Seybert, A. / Frangakis, A. / Pos, K.M.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB807 Germany
German Research Foundation (DFG)EXC115 Germany
German Research Foundation (DFG)FR-1653/12 Germany
German Research Foundation (DFG)SFB902 Germany
Innovative Medicines Initiative115525European Union
CitationJournal: Nat Commun / Year: 2021
Title: Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.
Authors: Alina Ornik-Cha / Julia Wilhelm / Jessica Kobylka / Hanno Sjuts / Attilio V Vargiu / Giuliano Malloci / Julian Reitz / Anja Seybert / Achilleas S Frangakis / Klaas M Pos /
Abstract: Upon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H/drug antiporter module that recognizes structurally diverse ...Upon antibiotic stress Gram-negative pathogens deploy resistance-nodulation-cell division-type tripartite efflux pumps. These include a H/drug antiporter module that recognizes structurally diverse substances, including antibiotics. Here, we show the 3.5 Å structure of subunit AdeB from the Acinetobacter baumannii AdeABC efflux pump solved by single-particle cryo-electron microscopy. The AdeB trimer adopts mainly a resting state with all protomers in a conformation devoid of transport channels or antibiotic binding sites. However, 10% of the protomers adopt a state where three transport channels lead to the closed substrate (deep) binding pocket. A comparison between drug binding of AdeB and Escherichia coli AcrB is made via activity analysis of 20 AdeB variants, selected on basis of side chain interactions with antibiotics observed in the AcrB periplasmic domain X-ray co-structures with fusidic acid (2.3 Å), doxycycline (2.1 Å) and levofloxacin (2.7 Å). AdeABC, compared to AcrAB-TolC, confers higher resistance to E. coli towards polyaromatic compounds and lower resistance towards antibiotic compounds.
History
DepositionDec 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Assembly

Deposited unit
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter


Theoretical massNumber of molelcules
Total (without water)345,4293
Polymers345,4293
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis, homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area18160 Å2
ΔGint-84 kcal/mol
Surface area112740 Å2
MethodPISA

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Components

#1: Protein Efflux pump membrane transporter


Mass: 115143.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AYE) (bacteria)
Strain: AYE / Gene: adeB, ABAYE1822 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: B0V4F5

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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: Homotrimeric RND-transporter AdeB reconstituted in Salipro
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.345 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AYE (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C43 (DE3)
Buffer solutionpH: 8.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HCl pH 8.51
2150 mMsodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 48

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34890 / Symmetry type: POINT
Atomic model buildingSpace: REAL

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