7B8P

Acinetobacter baumannii multidrug transporter AdeB in OOO state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.

Ornik-Cha, A.Wilhelm, J.Kobylka, J.Sjuts, H.Vargiu, A.V.Malloci, G.Reitz, J.Seybert, A.Frangakis, A.S.Pos, K.M.

(2021) Nat Commun 12: 6919-6919

  • DOI: https://doi.org/10.1038/s41467-021-27146-2
  • Primary Citation of Related Structures:  
    7B8P, 7B8Q, 7B8R, 7B8S, 7B8T

  • PubMed 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 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.


  • Organizational Affiliation

    Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Efflux pump membrane transporter
A, B, C
1,056Acinetobacter baumannii AYEMutation(s): 0 
Gene Names: adeBABAYE1822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.54 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB807
German Research Foundation (DFG)GermanyEXC115
German Research Foundation (DFG)GermanyFR-1653/12
German Research Foundation (DFG)GermanySFB902
Innovative Medicines InitiativeEuropean Union115525

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-20
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2021-12-08
    Changes: Database references
  • Version 1.3: 2024-07-10
    Changes: Data collection