Biological Assembly 1  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 367.13 kDa 
• Atom Count: 21,287 
• Modelled Residue Count: 2,448 
• Deposited Residue Count: 2,900 
• Unique protein chains: 1

 8FOA

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

• PDB DOI:  https://doi.org/10.2210/pdb8FOA/pdb
• EM Map EMD-29343: EMDB EMDataResource

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


• 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.66 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 37160865 
• 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.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 6	A, B, C, D	725	Homo sapiens	Mutation(s): 0  Gene Names: TRPV6, ECAC2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1D0 (Homo sapiens) Explore Q9H1D0  Go to UniProtKB:  Q9H1D0
PHAROS:  Q9H1D0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV	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	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)	EB [auth D], T [auth A]	GENISTEIN C15 H10 O5 TZBJGXHYKVUXJN-UHFFFAOYSA-N
ZN	R [auth A], RA [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Neuberger, A., Yelshanskaya, M.V., Nadezhdin, K.D., Sobolevsky, A.I.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01 NS107253
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)	United States	R01 AR078814
German Research Foundation (DFG)	Germany	464295817

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release