6B5V

Structure of TRPV5 in complex with econazole


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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 basis of TRPV5 channel inhibition by econazole revealed by cryo-EM.

Hughes, T.E.T.Lodowski, D.T.Huynh, K.W.Yazici, A.Del Rosario, J.Kapoor, A.Basak, S.Samanta, A.Han, X.Chakrapani, S.Zhou, Z.H.Filizola, M.Rohacs, T.Han, S.Moiseenkova-Bell, V.Y.

(2018) Nat Struct Mol Biol 25: 53-60

  • DOI: 10.1038/s41594-017-0009-1
  • Primary Citation of Related Structures:  
    6B5V

  • PubMed Abstract: 
  • The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca 2+ , that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca 2+ reabsorption ...

    The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca 2+ , that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca 2+ reabsorption. Here we present the structure of the full-length rabbit TRPV5 channel as determined using cryo-EM in complex with its inhibitor econazole. This structure reveals that econazole resides in a hydrophobic pocket analogous to that occupied by phosphatidylinositides and vanilloids in TRPV1, thus suggesting conserved mechanisms for ligand recognition and lipid binding among TRPV channels. The econazole-bound TRPV5 structure adopts a closed conformation with a distinct lower gate that occludes Ca 2+ permeation through the channel. Structural comparisons between TRPV5 and other TRPV channels, complemented with molecular dynamics (MD) simulations of the econazole-bound TRPV5 structure, allowed us to gain mechanistic insight into TRPV5 channel inhibition by small molecules.


    Organizational Affiliation

    Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. vmb@pennmedicine.upenn.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 5A, B, D [auth C], C [auth D]730Oryctolagus cuniculusMutation(s): 0 
Gene Names: Trpv5Ecac1
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Channels: Transient Receptor Potential (TRP)
Protein: 
TRPV5 Ca2+-selective ion channel with econazole inhibitor
Find proteins for Q9XSM3 (Oryctolagus cuniculus)
Explore Q9XSM3 
Go to UniProtKB:  Q9XSM3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ECL
Query on ECL

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], H [auth D], I [auth C]1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole
C18 H15 Cl3 N2 O
LEZWWPYKPKIXLL-SFHVURJKSA-N
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIGMS 1R01GM103899-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Author supporting evidence
  • Version 1.2: 2018-01-31
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence