[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural mechanism of heat-induced opening of a temperature-sensitive TRP channel.
Journal, issue, pagesNat Struct Mol Biol, Vol. 28, Issue 7, Page 564-572, Year 2021
Publish dateJul 8, 2021
AuthorsKirill D Nadezhdin / Arthur Neuberger / Yuri A Trofimov / Nikolay A Krylov / Viktor Sinica / Nikita Kupko / Viktorie Vlachova / Eleonora Zakharian / Roman G Efremov / Alexander I Sobolevsky /
PubMed AbstractNumerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been ...Numerous physiological functions rely on distinguishing temperature through temperature-sensitive transient receptor potential channels (thermo-TRPs). Although the function of thermo-TRPs has been studied extensively, structural determination of their heat- and cold-activated states has remained a challenge. Here, we present cryo-EM structures of the nanodisc-reconstituted wild-type mouse TRPV3 in three distinct conformations: closed, heat-activated sensitized and open states. The heat-induced transformations of TRPV3 are accompanied by changes in the secondary structure of the S2-S3 linker and the N and C termini and represent a conformational wave that links these parts of the protein to a lipid occupying the vanilloid binding site. State-dependent differences in the behavior of bound lipids suggest their active role in thermo-TRP temperature-dependent gating. Our structural data, supported by physiological recordings and molecular dynamics simulations, provide an insight for understanding the molecular mechanism of temperature sensing.
External linksNat Struct Mol Biol / PubMed:34239124 / PubMed Central
MethodsEM (single particle)
Resolution1.98 - 3.86 Å
Structure data

EMDB-23853, PDB-7mij:
Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 4 degrees Celsius
Method: EM (single particle) / Resolution: 1.98 Å

EMDB-23854, PDB-7mik:
Mouse TRPV3 in MSP2N2 nanodiscs, closed state at 42 degrees Celsius
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-23855, PDB-7mil:
Mouse TRPV3 in MSP2N2 nanodiscs, sensitized state at 42 degrees Celsius
Method: EM (single particle) / Resolution: 3.86 Å

EMDB-23856, PDB-7mim:
Mouse TRPV3 in cNW11 nanodiscs, closed state at 4 degrees Celsius
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-23857, PDB-7min:
Mouse TRPV3 in cNW11 nanodiscs, closed state at 42 degrees Celsius
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-23858, PDB-7mio:
Mouse TRPV3 in cNW11 nanodiscs, open state at 42 degrees Celsius
Method: EM (single particle) / Resolution: 3.48 Å

Chemicals

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • mus musculus (house mouse)
KeywordsMEMBRANE PROTEIN / Transient Receptor Potential V Family Member 3 / TRP channel / TRPV3 / closed state at 4 degrees Celsius / MSP2N2 / closed state at 42 degrees Celsius / sensitized state at 42 degrees Celsius / cNW11 / open state at 42 degrees Celsius

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more