9JE5 | pdb_00009je5

Cryo-EM structure of human TRPV3 in complex with citronellal determined in MSP2N2 nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Plant essential oil targets TRPV3 for skin renewal and structural mechanism of action.

Li, Y.Lu, X.Cheng, X.Xia, K.Hu, J.Wang, P.Pang, P.Gao, B.Sun, D.Zhang, Z.Li, D.Deng, Z.Tian, C.Xie, C.Yao, J.

(2025) Nat Commun 16: 2728-2728

  • DOI: https://doi.org/10.1038/s41467-025-58033-9
  • Primary Citation of Related Structures:  
    9JDM, 9JE5, 9JEE, 9JEF, 9JEG

  • PubMed Abstract: 

    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.


  • Organizational Affiliation
    • State Key Laboratory of Virology and Biosafety, TaiKang Center for Life and Medical Sciences, College of Life Sciences, Hubei Key Laboratory of Cell Homeostasis, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 3
A, B, C, D
799Homo sapiensMutation(s): 1 
Gene Names: TRPV3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NET8 (Homo sapiens)
Explore Q8NET8 
Go to UniProtKB:  Q8NET8
PHAROS:  Q8NET8
GTEx:  ENSG00000167723 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NET8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AA [auth D]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
A1EBV (Subject of Investigation/LOI)
Query on A1EBV

Download Ideal Coordinates CCD File 
BA [auth D],
I [auth A],
P [auth B],
V [auth C]
(3~{S})-3,7-dimethyloct-6-enal
C10 H18 O
NEHNMFOYXAPHSD-JTQLQIEISA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2025-03-26 
  • Deposition Author(s): Lu, X., Yao, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-16
    Changes: Data collection