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	Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 2874, Year 2022
Publish date	May 24, 2022
Authors	Do Hoon Kwon / Feng Zhang / Justin G Fedor / Yang Suo / Seok-Yong Lee /
PubMed Abstract	Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational ...Single particle cryo-EM often yields multiple protein conformations within a single dataset, but experimentally deducing the temporal relationship of these conformers within a conformational trajectory is not trivial. Here, we use thermal titration methods and cryo-EM in an attempt to obtain temporal resolution of the conformational trajectory of the vanilloid receptor TRPV1 with resiniferatoxin (RTx) bound. Based on our cryo-EM ensemble analysis, RTx binding to TRPV1 appears to induce intracellular gate opening first, followed by selectivity filter dilation, then pore loop rearrangement to reach the final open state. This apparent conformational wave likely arises from the concerted, stepwise, additive structural changes of TRPV1 over many subdomains. Greater understanding of the RTx-mediated long-range allostery of TRPV1 could help further the therapeutic potential of RTx, which is a promising drug candidate for pain relief associated with advanced cancer or knee arthritis.
External links	Nat Commun / PubMed:35610228 / PubMed Central
Methods	EM (single particle)
Resolution	3.04 - 3.45 Å
Structure data	24636 7rqu EMDB-24636, PDB-7rqu: Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in a closed state, class I Method: EM (single particle) / Resolution: 3.05 Å 24637 7rqv EMDB-24637, PDB-7rqv: Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an intermediate-closed state, class II Method: EM (single particle) / Resolution: 3.45 Å 24638 7rqw EMDB-24638, PDB-7rqw: Cryo-EM structure of the full-length TRPV1 with RTx at 4 degrees Celsius, in an open state, class III Method: EM (single particle) / Resolution: 3.11 Å 24639 7rqx EMDB-24639, PDB-7rqx: Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an intermediate-open state, class A Method: EM (single particle) / Resolution: 3.36 Å 24640 7rqy EMDB-24640, PDB-7rqy: Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an open state, class B Method: EM (single particle) / Resolution: 3.04 Å 24641 7rqz EMDB-24641, PDB-7rqz: Cryo-EM structure of the full-length TRPV1 with RTx at 48 degrees Celsius, in an open state, class alpha Method: EM (single particle) / Resolution: 3.32 Å
Chemicals	ChemComp-6EU: resiniferatoxin / toxinYM ChemComp-LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipidYM ChemComp-6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipidYM ChemComp-YFP: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol ChemComp-NA: Unknown entry ChemComp-PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipidYM
Source	rattus norvegicus (Norway rat)
Keywords	MEMBRANE PROTEIN / ligand-gating ion channel