8FOA

Cryo-EM structure of human TRPV6 in complex with the natural phytoestrogen genistein

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

  • Deposited: 2022-12-30 Released: 2023-05-24 
  • 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: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural mechanism of human oncochannel TRPV6 inhibition by the natural phytoestrogen genistein.

Neuberger, A.Trofimov, Y.A.Yelshanskaya, M.V.Nadezhdin, K.D.Krylov, N.A.Efremov, R.G.Sobolevsky, A.I.

(2023) Nat Commun 14: 2659-2659

  • DOI: https://doi.org/10.1038/s41467-023-38352-5
  • Primary Citation of Related Structures:  
    8FOA, 8FOB

  • PubMed Abstract: 

    Calcium-selective oncochannel TRPV6 is the major driver of cell proliferation in human cancers. While significant effort has been invested in the development of synthetic TRPV6 inhibitors, natural channel blockers have been largely neglected. Here we report the structure of human TRPV6 in complex with the plant-derived phytoestrogen genistein, extracted from Styphnolobium japonicum, that was shown to inhibit cell invasion and metastasis in cancer clinical trials. Despite the pharmacological value, the molecular mechanism of TRPV6 inhibition by genistein has remained enigmatic. We use cryo-EM combined with electrophysiology, calcium imaging, mutagenesis, and molecular dynamics simulations to show that genistein binds in the intracellular half of the TRPV6 pore and acts as an ion channel blocker and gating modifier. Genistein binding to the open channel causes pore closure and a two-fold symmetrical conformational rearrangement in the S4-S5 and S6-TRP helix regions. The unprecedented mechanism of TRPV6 inhibition by genistein uncovers new possibilities in structure-based drug design.


  • 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
725Homo 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]
BA [auth B]
BB [auth D]
CA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
BB [auth D],
CA [auth B],
CB [auth D],
DA [auth B],
DB [auth D],
EA [auth B],
FA [auth B],
GA [auth B],
H [auth A],
HA [auth C],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
PA [auth C],
Q [auth A],
QA [auth C],
SA [auth D],
TA [auth D],
U [auth B],
UA [auth D],
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]
IA [auth C]
JA [auth C]
E [auth A],
F [auth A],
G [auth A],
IA [auth C],
JA [auth C],
KA [auth C],
P [auth A],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
GEN (Subject of Investigation/LOI)
Query on GEN

Download Ideal Coordinates CCD File 
EB [auth D],
T [auth A]
GENISTEIN
C15 H10 O5
TZBJGXHYKVUXJN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
R [auth A],
RA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
S [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.3

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: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection, Refinement description