8SP8

Human TRP channel TRPV6 in cNW30 nanodiscs inhibited by tetrahydrocannabivarin (THCV)

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

  • Deposited: 2023-05-02 Released: 2023-08-23 
  • Deposition Author(s): Neuberger, A., Yelshanskaya, M.V., Nadezhdin, K.D., Sobolevsky, A.I.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular pathway and structural mechanism of human oncochannel TRPV6 inhibition by the phytocannabinoid tetrahydrocannabivarin.

Neuberger, A.Trofimov, Y.A.Yelshanskaya, M.V.Khau, J.Nadezhdin, K.D.Khosrof, L.S.Krylov, N.A.Efremov, R.G.Sobolevsky, A.I.

(2023) Nat Commun 14: 4630-4630

  • DOI: https://doi.org/10.1038/s41467-023-40362-2
  • Primary Citation of Related Structures:  
    8SP8

  • PubMed Abstract: 

    The calcium-selective oncochannel TRPV6 is an important driver of cell proliferation in human cancers. Despite increasing interest of pharmacological research in developing synthetic inhibitors of TRPV6, natural compounds acting at this channel have been largely neglected. On the other hand, pharmacokinetics of natural small-molecule antagonists optimized by nature throughout evolution endows these compounds with a medicinal potential to serve as potent and safe next-generation anti-cancer drugs. Here we report the structure of human TRPV6 in complex with tetrahydrocannabivarin (THCV), a natural cannabinoid inhibitor extracted from Cannabis sativa. We use cryo-electron microscopy combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to identify THCV binding sites in the portals that connect the membrane environment surrounding the protein to the central cavity of the channel pore and to characterize the allosteric mechanism of TRPV6 inhibition. We also propose the molecular pathway taken by THCV to reach its binding site. Our study provides a foundation for the development of new TRPV6-targeting drugs.


  • 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 6
A, B, C, D
666Homo sapiensMutation(s): 0 
Gene Names: TRPV6ECAC2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1D0 (Homo sapiens)
Explore Q9H1D0 
Go to UniProtKB:  Q9H1D0
PHAROS:  Q9H1D0
GTEx:  ENSG00000165125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H1D0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
CA [auth B]
DA [auth B]
EA [auth C]
AA [auth B],
AB [auth D],
CA [auth B],
DA [auth B],
EA [auth C],
H [auth A],
I [auth A],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
O [auth A],
OA [auth C],
PA [auth C],
QA [auth D],
RA [auth D],
S [auth B],
SA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
Y01
Query on Y01

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
GA [auth C]
HA [auth C]
E [auth A],
F [auth A],
G [auth A],
GA [auth C],
HA [auth C],
IA [auth C],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
I8E (Subject of Investigation/LOI)
Query on I8E

Download Ideal Coordinates CCD File 
BA [auth B]
BB [auth D]
FA [auth C]
L [auth A]
NA [auth C]
BA [auth B],
BB [auth D],
FA [auth C],
L [auth A],
NA [auth C],
P [auth A],
T [auth B],
TA [auth D]
Tetrahydrocannabivarin
C19 H26 O2
ZROLHBHDLIHEMS-HUUCEWRRSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
Q [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
R [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
I8E BindingDB:  8SP8 IC50: 9400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
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
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814
German Research Foundation (DFG)Germany464295817

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release