7RAU | pdb_00007rau

Structure of TRPV3 in complex with osthole

PDB DOI: https://doi.org/10.2210/pdb7RAU/pdb
EM Map EMD-24386: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2021-07-02 Released: 2021-09-08
Deposition Author(s): Neuberger, A., 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 Science Foundation (NSF, United States), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural mechanism of TRPV3 channel inhibition by the plant-derived coumarin osthole.

Neuberger, A., Nadezhdin, K.D., Zakharian, E., Sobolevsky, A.I.

(2021) EMBO Rep 22: e53233-e53233

PubMed: 34472684 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.15252/embr.202153233
Primary Citation Related Structures:
7RAS, 7RAU

PubMed Abstract:
TRPV3, a representative of the vanilloid subfamily of TRP channels, is predominantly expressed in skin keratinocytes and has been implicated in cutaneous sensation and associated with numerous skin pathologies and cancers. TRPV3 is inhibited by the natural coumarin derivative osthole, an active ingredient of Cnidium monnieri, which has been used in traditional Chinese medicine for the treatment of a variety of human diseases. However, the structural basis of channel inhibition by osthole has remained elusive. Here we present cryo-EM structures of TRPV3 in complex with osthole, revealing two types of osthole binding sites in the transmembrane region of TRPV3 that coincide with the binding sites of agonist 2-APB. Osthole binding converts the channel pore into a previously unidentified conformation with a widely open selectivity filter and closed intracellular gate. Our structures provide insight into competitive inhibition of TRPV3 by osthole and can serve as a template for the design of osthole chemistry-inspired drugs targeting TRPV3-associated diseases.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 371.88 kDa
Atom Count: 20,000
Modeled Residue Count: 2,440
Deposited Residue Count: 3,232
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 3	A, B, C, D	808	Mus musculus	Mutation(s): 1 Gene Names: Trpv3 Membrane Entity: Yes
UniProt
Find proteins for Q8K424 (Mus musculus) Explore Q8K424 Go to UniProtKB: Q8K424
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8K424
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A0O (Subject of Investigation/LOI) Query on A0O Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth C] E [auth A], F [auth A], G [auth B], H [auth B], I [auth C], J [auth C], K [auth D], L [auth D]	7-methoxy-8-(3-methylbut-2-enyl)chromen-2-one C₁₅ H₁₆ O₃ MBRLOUHOWLUMFF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.99 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	2.14

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Neuberger, A.

Nadezhdin, K.D.

Sobolevsky, A.I.

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 Science Foundation (NSF, United States)	United States	1818086
German Research Foundation (DFG)	Germany	464295817