8FPF

Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to ATP: BmrCD_IF-ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter

Qingyu, T.Hassane, M.

(2023) Nat Commun 14: 7184-7184

  • DOI: https://doi.org/10.1038/s41467-023-42937-5
  • Primary Citation of Related Structures:  
    8FHK, 8FMV, 8FPF, 8SZC, 8T1P, 8T3K

  • PubMed Abstract: 

    Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg 2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.


  • Organizational Affiliation

    Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable multidrug resistance ABC transporter ATP-binding/permease protein YheHA [auth D]681Bacillus subtilis subsp. subtilis str. 168Mutation(s): 4 
Gene Names: yheHBSU09720
EC: 7.6.2
Membrane Entity: Yes 
UniProt
Find proteins for O07549 (Bacillus subtilis (strain 168))
Explore O07549 
Go to UniProtKB:  O07549
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07549
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Probable multidrug resistance ABC transporter ATP-binding/permease protein YheIB [auth C]607Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: yheIBSU09710
EC: 7.6.2
Membrane Entity: Yes 
UniProt
Find proteins for O07550 (Bacillus subtilis (strain 168))
Explore O07550 
Go to UniProtKB:  O07550
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07550
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
C [auth D]
D
E [auth D]
AA [auth C],
BA [auth C],
C [auth D],
D,
E [auth D],
F [auth D],
G [auth D],
H [auth D],
I [auth D],
J [auth D],
K [auth D],
L [auth D],
M [auth D],
N [auth D],
O [auth D],
P [auth D],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth C],
Q [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIGMS R01-128087

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release