[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

TitlePlant essential oil targets TRPV3 for skin renewal and structural mechanism of action.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2728, Year 2025
Publish dateMar 19, 2025
AuthorsYang Li / Xuteng Lu / Xufeng Cheng / Keyu Xia / Junyan Hu / Peiyu Wang / Peiyuan Pang / Bomin Gao / Demeng Sun / Zhuzhen Zhang / Dongdong Li / Zengqin Deng / Changlin Tian / Chang Xie / Jing Yao /
PubMed AbstractOur skin safeguards the body homeostasis for health and also provides psychological consolation in social life. Natural essential oils are widely used for skin maintenance, while the molecular target ...Our skin safeguards the body homeostasis for health and also provides psychological consolation in social life. Natural essential oils are widely used for skin maintenance, while the molecular target and mechanism of action remain largely unknown. Here, we report that citronellal, a plant-derived acyclic monoterpene commonly used for personal care, stimulates skin renewal by promoting keratinocyte proliferation through the activation of TRPV3. We further present cryo-EM structures of human TRPV3 in complex with acyclic monoterpenes, including citronellal, citral, linalool and isodihydrolavandulal, determined at resolutions of 3.1-3.6 Å. Our structural and functional analysis unmasks consistent yet subtly different binding modes within the TRPV3 vanilloid site. Our results elucidate that essential oil ligands activate TRPV3 channels by competitively displacing endogenous lipids from the vanilloid site. Together, these findings identify TRPV3 as the molecular target of natural acyclic monoterpenes for skin renewal, and delineate the structural basis of action, thus being instrumental for moving forward skin healthcare.
External linksNat Commun / PubMed:40108208 / PubMed Central
MethodsEM (single particle)
Resolution3.13 - 3.62 Å
Structure data

EMDB-61396, PDB-9jdm:
Cryo-EM structure of human TRPV3 determined in MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-61407, PDB-9je5:
Cryo-EM structure of human TRPV3 in complex with citronellal determined in MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-61414, PDB-9jee:
Cryo-EM structure of human TRPV3 in complex with citral determined in MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-61415, PDB-9jef:
Cryo-EM structure of human TRPV3 in complex with linalool determined in MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-61416, PDB-9jeg:
Cryo-EM structure of human TRPV3 in complex with isodihydrolavandulal determined in MSP2N2 nanodisc
Method: EM (single particle) / Resolution: 3.39 Å

Chemicals

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

PDB-1ebv:
OVINE PGHS-1 COMPLEXED WITH SALICYL HYDROXAMIC ACID

ChemComp-GRQ:
Geranaldehyde

PDB-1ebl:
THE 1.8 A CRYSTAL STRUCTURE AND ACTIVE SITE ARCHITECTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE III (FABH) FROM ESCHERICHIA COLI

PDB-1ebm:
CRYSTAL STRUCTURE OF THE HUMAN 8-OXOGUANINE GLYCOSYLASE (HOGG1) BOUND TO A SUBSTRATE OLIGONUCLEOTIDE

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN

+
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