8V6L

Open-state cryo-EM structure of human TRPV3 in presence of tetrahydrocannabivarin (THCV) in cNW30 nanodiscs

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMMemProtMD

  • Deposited: 2023-12-01 Released: 2024-04-17 
  • Deposition Author(s): Nadezhdin, K.D., Neuberger, A., Sobolevsky, A.I.
  • Funding Organization(s): National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 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

TRPV3 activation by different agonists accompanied by lipid dissociation from the vanilloid site.

Nadezhdin, K.D.Neuberger, A.Khosrof, L.S.Talyzina, I.A.Khau, J.Yelshanskaya, M.V.Sobolevsky, A.I.

(2024) Sci Adv 10: eadn2453-eadn2453

  • DOI: https://doi.org/10.1126/sciadv.adn2453
  • Primary Citation of Related Structures:  
    8V6K, 8V6L, 8V6M, 8V6N, 8V6O

  • PubMed Abstract: 

    TRPV3 represents both temperature- and ligand-activated transient receptor potential (TRP) channel. Physiologically relevant opening of TRPV3 channels by heat has been captured structurally, while opening by agonists has only been observed in structures of mutant channels. Here, we present cryo-EM structures that illuminate opening and inactivation of wild-type human TRPV3 in response to binding of two types of agonists: either the natural cannabinoid tetrahydrocannabivarin (THCV) or synthetic agonist 2-aminoethoxydiphenylborane (2-APB). We found that THCV binds to the vanilloid site, while 2-APB binds to the S1-S4 base and ARD-TMD linker sites. Despite binding to distally located sites, both agonists induce similar pore opening and cause dissociation of a lipid that occupies the vanilloid site in their absence. Our results uncover different but converging allosteric pathways through which small-molecule agonists activate TRPV3 and provide a framework for drug design and understanding the role of lipids in ion channel function.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


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
808Homo sapiensMutation(s): 0 
Gene Names: TRPV3
Membrane Entity: Yes 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
S [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Z [auth C]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
I8E (Subject of Investigation/LOI)
Query on I8E

Download Ideal Coordinates CCD File 
EA [auth D],
H [auth A],
R [auth B],
Y [auth C]
Tetrahydrocannabivarin
C19 H26 O2
ZROLHBHDLIHEMS-HUUCEWRRSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
T [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I8E BindingDB:  8V6L IC50: 3000 (nM) from 1 assay(s)
EC50: 3800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
German Research Foundation (DFG)Germany464295817

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary