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TitleVanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 2874, Year 2022
Publish dateMay 24, 2022
AuthorsDo Hoon Kwon / Feng Zhang / Justin G Fedor / Yang Suo / Seok-Yong Lee /
PubMed AbstractSingle 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 linksNat Commun / PubMed:35610228 / PubMed Central
MethodsEM (single particle)
Resolution3.04 - 3.45 Å
Structure data

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

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

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

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

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

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 / toxin*YM

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

ChemComp-YFP:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol

ChemComp-NA:
Unknown entry

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

Source
  • rattus norvegicus (Norway rat)
KeywordsMEMBRANE PROTEIN / ligand-gating ion channel

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