7T37 | pdb_00007t37

Activated state of 2-APB and CBD-bound wildtype rat TRPV2 in nanodiscs

PDB DOI: https://doi.org/10.2210/pdb7T37/pdb
EM Map EMD-25650: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Rattus norvegicus
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2021-12-07 Released: 2022-05-04
Deposition Author(s): Pumroy, R.A., Protopopova, A.D., Gallo, P.N., Moiseenkova-Bell, V.Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 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

Structural insights into TRPV2 activation by small molecules.

Pumroy, R.A., Protopopova, A.D., Fricke, T.C., Lange, I.U., Haug, F.M., Nguyen, P.T., Gallo, P.N., Sousa, B.B., Bernardes, G.J.L., Yarov-Yarovoy, V., Leffler, A., Moiseenkova-Bell, V.Y.

(2022) Nat Commun 13: 2334-2334

PubMed: 35484159 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-30083-3
Primary Citation Related Structures:
7N0M, 7N0N, 7T37, 7T38

PubMed Abstract:
Transient receptor potential vanilloid 2 (TRPV2) is involved in many critical physiological and pathophysiological processes, making it a promising drug target. Here we present cryo-electron microscopy (cryo-EM) structures of rat TRPV2 in lipid nanodiscs activated by 2-aminoethoxydiphenyl borate (2-APB) and propose a TRPV2-specific 2-ABP binding site at the interface of S5 of one monomer and the S4-S5 linker of the adjacent monomer. In silico docking and electrophysiological studies confirm the key role of His521 and Arg539 in 2-APB activation of TRPV2. Additionally, electrophysiological experiments show that the combination of 2-APB and cannabidiol has a synergetic effect on TRPV2 activation, and cryo-EM structures demonstrate that both drugs were able to bind simultaneously. Together, our cryo-EM structures represent multiple functional states of the channel, providing a native picture of TRPV2 activation by small molecules and a structural framework for the development of TRPV2-specific activators.

Organizational Affiliation

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States.

Macromolecule Content

Total Structure Weight: 349.35 kDa
Atom Count: 20,176
Modeled Residue Count: 2,476
Deposited Residue Count: 3,044
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 2	A, B, C, D	761	Rattus norvegicus	Mutation(s): 0 Gene Names: Trpv2, Sac2b, Vrl1 Membrane Entity: Yes
UniProt
Find proteins for Q9WUD2 (Rattus norvegicus) Explore Q9WUD2 Go to UniProtKB: Q9WUD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WUD2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P0T (Subject of Investigation/LOI) Query on P0T Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], L [auth D]	cannabidiol C₂₁ H₃₀ O₂ QHMBSVQNZZTUGM-ZWKOTPCHSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain L [auth D]
FZ4 (Subject of Investigation/LOI) Query on FZ4 Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth D]	2-aminoethyl diphenylborinate C₁₄ H₁₆ B N O BLZVCIGGICSWIG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
P0T	BindingDB: 7T37	IC50: 1100 (nM) from 1 assay(s)
P0T	BindingDB: 7T37	EC50: 1200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Pumroy, R.A.

Protopopova, A.D.

Gallo, P.N.

Moiseenkova-Bell, V.Y.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM103899
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM129357