6R72

Crystal structure of BmrA-E504A in an outward-facing conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Multidrug exporter ATP-binding cassette
A, B, C, D
599Bacillus subtilisMutation(s): 1 
Gene Names: B4417_3307
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.95 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.263 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.805α = 90
b = 110.754β = 93.23
c = 155.615γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-18-CE11-0002-01
French National Research AgencyFranceANR-CE11-0015-03
Ligue Regionale Contre le CancerFrance189393

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references, Derived calculations
  • Version 1.2: 2022-02-02
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description