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	Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 2967, Year 2024
Publish date	Apr 5, 2024
Authors	Nikhil Bharambe / Zhuowen Li / David Seiferth / Asha Manikkoth Balakrishna / Philip C Biggin / Sandip Basak /
PubMed Abstract	GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite ...GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 - 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.
External links	Nat Commun / PubMed:38580666 / PubMed Central
Methods	EM (single particle)
Resolution	2.6476 - 3.42 Å
Structure data	35161 8i41 EMDB-35161, PDB-8i41: Cryo-EM structure of nanodisc (asolectin) reconstituted GLIC at pH 7.5 Method: EM (single particle) / Resolution: 3.42 Å 35162 8i42 EMDB-35162, PDB-8i42: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 7.5 Method: EM (single particle) / Resolution: 2.92 Å 35163 8i47 EMDB-35163, PDB-8i47: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 5.5 Method: EM (single particle) / Resolution: 2.7 Å 35164 8i48 EMDB-35164, PDB-8i48: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in closed state Method: EM (single particle) / Resolution: 2.74 Å 36339 8jj3 EMDB-36339, PDB-8jj3: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 2.5 Method: EM (single particle) / Resolution: 2.6476 Å 37446 8wcq EMDB-37446, PDB-8wcq: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in intermediate state Method: EM (single particle) / Resolution: 3.35 Å 37447 8wcr EMDB-37447, PDB-8wcr: Cryo-EM structure of nanodisc (PE:PS:PC) reconstituted GLIC at pH 4 in open state Method: EM (single particle) / Resolution: 2.74 Å
Chemicals	ChemComp-PLC: DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipidYM ChemComp-PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE, phospholipidYM / Discrete optimized protein energy ChemComp-HOH: WATER / Water ChemComp-CL: Unknown entry / Chloride
Source	gloeobacter violaceus (bacteria)
Keywords	MEMBRANE PROTEIN / pentameric ligand-gated ion channels / cis-loop / cryo-EM / nanodisc