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	Conformation space of a heterodimeric ABC exporter under turnover conditions.
Journal, issue, pages	Nature, Vol. 571, Issue 7766, Page 580-583, Year 2019
Publish date	Jul 17, 2019
Authors	Susanne Hofmann / Dovile Januliene / Ahmad R Mehdipour / Christoph Thomas / Erich Stefan / Stefan Brüchert / Benedikt T Kuhn / Eric R Geertsma / Gerhard Hummer / Robert Tampé / Arne Moeller /
PubMed Abstract	Cryo-electron microscopy (cryo-EM) has the capacity to capture molecular machines in action. ATP-binding cassette (ABC) exporters are highly dynamic membrane proteins that extrude a wide range of ...Cryo-electron microscopy (cryo-EM) has the capacity to capture molecular machines in action. ATP-binding cassette (ABC) exporters are highly dynamic membrane proteins that extrude a wide range of substances from the cytosol and thereby contribute to essential cellular processes, adaptive immunity and multidrug resistance. Despite their importance, the coupling of nucleotide binding, hydrolysis and release to the conformational dynamics of these proteins remains poorly resolved, especially for heterodimeric and/or asymmetric ABC exporters that are abundant in humans. Here we present eight high-resolution cryo-EM structures that delineate the full functional cycle of an asymmetric ABC exporter in a lipid environment. Cryo-EM analysis under active turnover conditions reveals distinct inward-facing (IF) conformations-one of them with a bound peptide substrate-and previously undescribed asymmetric post-hydrolysis states with dimerized nucleotide-binding domains and a closed extracellular gate. By decreasing the rate of ATP hydrolysis, we could capture an outward-facing (OF) open conformation-an otherwise transient state vulnerable to substrate re-entry. The ATP-bound pre-hydrolysis and vanadate-trapped states are conformationally equivalent; both comprise co-existing OF conformations with open and closed extracellular gates. By contrast, the post-hydrolysis states from the turnover experiment exhibit asymmetric ATP and ADP occlusion after phosphate release from the canonical site and display a progressive separation of the nucleotide-binding domains and unlocking of the intracellular gate. Our findings reveal that phosphate release, not ATP hydrolysis, triggers the return of the exporter to the IF conformation. By mapping the conformational landscape during active turnover, aided by mutational and chemical modulation of kinetic rates to trap the key intermediates, we resolved fundamental steps of the substrate translocation cycle of asymmetric ABC transporters.
External links	Nature / PubMed:31316210 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 4.2 Å
Structure data	4773 6raf EMDB-4773, PDB-6raf: Heterodimeric ABC exporter TmrAB in inward-facing narrow conformation under turnover conditions Method: EM (single particle) / Resolution: 3.8 Å 4774 6rag EMDB-4774, PDB-6rag: Heterodimeric ABC exporter TmrAB in inward-facing wide conformation under turnover conditions Method: EM (single particle) / Resolution: 4.2 Å 4775 6rah EMDB-4775, PDB-6rah: Heterodimeric ABC exporter TmrAB in ATP-bound outward-facing open conformation Method: EM (single particle) / Resolution: 2.8 Å 4776 6rai EMDB-4776, PDB-6rai: Heterodimeric ABC exporter TmrAB in ATP-bound outward-facing occluded conformation Method: EM (single particle) / Resolution: 2.9 Å 4777 6raj EMDB-4777, PDB-6raj: Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing open conformation Method: EM (single particle) / Resolution: 3.5 Å 4778 6rak EMDB-4778, PDB-6rak: Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing occluded conformation Method: EM (single particle) / Resolution: 3.3 Å 4779 6ral EMDB-4779, PDB-6ral: Heterodimeric ABC exporter TmrAB under turnover conditions in asymmetric unlocked return conformation Method: EM (single particle) / Resolution: 3.5 Å 4780 6ram EMDB-4780, PDB-6ram: Heterodimeric ABC exporter TmrAB under turnover conditions in asymmetric unlocked return conformation with wider opened intracellular gate Method: EM (single particle) / Resolution: 3.8 Å 4781 6ran EMDB-4781: Heterodimeric ABC exporter TmrAB with bound peptide substrate in inward-facing wide conformation PDB-6ran: Heterodimeric ABC exporter TmrAB in inward-facing wide conformation Method: EM (single particle) / Resolution: 4.2 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-MG: Unknown entry ChemComp-HOH: WATER / Water ChemComp-AOV: ADP ORTHOVANADATE / energy-carrying molecule analogue*YM
Source	thermus thermophilus hb27 (bacteria) thermus thermophilus (bacteria) vicugna pacos (alpaca)
Keywords	TRANSPORT PROTEIN / ATP-binding cassette transporter / membrane protein / heterodimer / exporter / ABC transporter / nucleotide binding domains