[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 mechanisms of TRPV2 modulation by endogenous and exogenous ligands.
Journal, issue, pagesNat Chem Biol, Vol. 19, Issue 1, Page 72-80, Year 2023
Publish dateSep 26, 2022
AuthorsNannan Su / Wenxuan Zhen / Heng Zhang / Lingyi Xu / Yitian Jin / Xiaoying Chen / Cheng Zhao / Qinrui Wang / Xinyan Wang / Shaowei Li / Han Wen / Wei Yang / Jiangtao Guo / Fan Yang /
PubMed AbstractThe transient receptor potential vanilloid 2 (TRPV2) ion channel is a polymodal receptor widely involved in many physiological and pathological processes. Despite many TRPV2 modulators being ...The transient receptor potential vanilloid 2 (TRPV2) ion channel is a polymodal receptor widely involved in many physiological and pathological processes. Despite many TRPV2 modulators being identified, whether and how TRPV2 is regulated by endogenous lipids remains elusive. Here, we report an endogenous cholesterol molecule inside the vanilloid binding pocket (VBP) of TRPV2, with a 'head down, tail up' configuration, resolved at 3.2 Å using cryo-EM. Cholesterol binding antagonizes ligand activation of TRPV2, which is removed from VBP by methyl-β-cyclodextrin (MβCD) as resolved at 2.9 Å. We also observed that estradiol (E2) potentiated TRPV2 activation by 2-aminoethoxydiphenyl borate (2-APB), a classic tool compound for TRP channels. Our cryo-EM structures (resolved at 2.8-3.3 Å) further suggest how E2 disturbed cholesterol binding and how 2-APB bound within the VBP with E2 or without both E2 and endogenous cholesterol, respectively. Therefore, our study has established the structural basis for ligand recognition of the inhibitory endogenous cholesterol and excitatory exogenous 2-APB in TRPV2.
External linksNat Chem Biol / PubMed:36163384
MethodsEM (single particle)
Resolution2.47 - 3.27 Å
Structure data

33156

7xem

EMDB-33156, PDB-7xem:
Cholesterol bound state of mTRPV2
Method: EM (single particle) / Resolution: 3.17 Å

33157

7xeo

EMDB-33157, PDB-7xeo:
MbetaCD treated state of mTRPV2
Method: EM (single particle) / Resolution: 2.89 Å

33158

7xer

EMDB-33158, PDB-7xer:
Structure of mTRPV2_Q525T
Method: EM (single particle) / Resolution: 2.47 Å

33159

7xeu

EMDB-33159, PDB-7xeu:
Structure of mTRPV2_E2
Method: EM (single particle) / Resolution: 2.77 Å

33160

7xev

EMDB-33160, PDB-7xev:
Structure of mTRPV2_2-APB
Method: EM (single particle) / Resolution: 3.27 Å

33161

7xew

EMDB-33161, PDB-7xew:
Structure of mTRPV2_Q525F
Method: EM (single particle) / Resolution: 2.59 Å

33774

7yep

EMDB-33774, PDB-7yep:
2-APB bound state of mTRPV2
Method: EM (single particle) / Resolution: 2.83 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL / Cholesterol

ChemComp-HOH:
WATER / Water

ChemComp-FZ4:
2-aminoethyl diphenylborinate / 2-Aminoethoxydiphenyl borate

Source
  • mus musculus (house mouse)
KeywordsSTRUCTURAL PROTEIN / mTRPV2 / chloesterol / MbetaCD / MEMBRANE PROTEIN / 2-APB

+
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