7OW8 | pdb_00007ow8

CryoEM structure of the ABC transporter BmrA E504A mutant in complex with ATP-Mg


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter.

Chaptal, V.Zampieri, V.Wiseman, B.Orelle, C.Martin, J.Nguyen, K.A.Gobet, A.Di Cesare, M.Magnard, S.Javed, W.Eid, J.Kilburg, A.Peuchmaur, M.Marcoux, J.Monticelli, L.Hogbom, M.Schoehn, G.Jault, J.M.Boumendjel, A.Falson, P.

(2022) Sci Adv 8: eabg9215-eabg9215

  • DOI: https://doi.org/10.1126/sciadv.abg9215
  • Primary Citation Related Structures: 
    6R72, 6R81, 7BG4, 7OW8

  • PubMed Abstract: 

    Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg 2+ -bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis . Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.


  • Organizational Affiliation
    • Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France.

Macromolecule Content 

  • Total Structure Weight: 132.04 kDa 
  • Atom Count: 8,942 
  • Modeled Residue Count: 1,154 
  • Deposited Residue Count: 1,192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Multidrug resistance ABC transporter ATP-binding/permease protein BmrA
A, B
596Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: bmrAyvcCBSU34820
EC: 7.6.2
Membrane Entity: Yes 
UniProt
Find proteins for O06967 (Bacillus subtilis (strain 168))
Explore O06967 
Go to UniProtKB:  O06967
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06967
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2
MODEL REFINEMENTISOLDE1.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-CLAMP- 13-BSV5-0001-01
Agence Nationale de la Recherche (ANR)FranceANR-NMX-14-CE09-0024-03
Agence Nationale de la Recherche (ANR)FranceANR-CAVEOTANK-17-CE11-0015-03
Agence Nationale de la Recherche (ANR)FranceANR-CLAMP2- 18-CE11-0002-01
Agence Nationale de la Recherche (ANR)FranceANR-19-CE11- 0023-01
French League Against CancerFrancecomite Ardeche 212471

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-02
    Changes: Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2025-07-09
    Changes: Data collection, Structure summary