Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter.
Journal, issue, pages	Nat Commun, Vol. 14, Issue 1, Page 7184, Year 2023
Publish date	Nov 8, 2023
Authors	Qingyu Tang / Matt Sinclair / Hale S Hasdemir / Richard A Stein / Erkan Karakas / Emad Tajkhorshid / Hassane S Mchaourab /
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 ...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 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.
External links	Nat Commun / PubMed:37938578 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 5.65 Å
Structure data	29087 8fhk EMDB-29087, PDB-8fhk: Heterodimeric ABC transporter BmrCD in the occluded conformation bound to ATP: BmrCD_OC-ATP Method: EM (single particle) / Resolution: 2.9 Å 29297 8fmv EMDB-29297: Structure0915 PDB-8fmv: Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to substrate and ATP: BmrCD_IF-2HT/ATP Method: EM (single particle) / Resolution: 3.34 Å 29362 8fpf EMDB-29362, PDB-8fpf: Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to ATP: BmrCD_IF-ATP Method: EM (single particle) / Resolution: 3.27 Å 40908 8szc EMDB-40908, PDB-8szc: Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to substrate and ATP: BmrCD_IF-1HT/ATP Method: EM (single particle) / Resolution: 3.06 Å 40974 8t1p EMDB-40974: BmrCD_OC-ADPVi PDB-8t1p: Heterodimeric ABC transporter BmrCD in the occluded conformation bound to ADPVi: BmrCD_OC-ADPVi Method: EM (single particle) / Resolution: 2.96 Å 41004 8t3k EMDB-41004, PDB-8t3k: Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to ATP: BmrCD_IF-ATP2 Method: EM (single particle) / Resolution: 3.33 Å EMDB-41058: Heterodimeric ABC transporter BmrCD in the inward-facing conformation bound to substrate and ADPVi: BmrCD_IF-HT/ADPVi Method: EM (single particle) / Resolution: 5.65 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipidYM / POPC ChemComp-MG: Unknown entry ChemComp-HT1: 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE / Bisbenzimide ChemComp-AOV: ADP ORTHOVANADATE / energy-carrying molecule analogue*YM
Source	bacillus subtilis subsp. subtilis str. 168 (bacteria)
Keywords	TRANSLOCASE / transporter / complex / lipids / MEMBRANE PROTEIN / Transport protein