Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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: 333.17 kDa 
• Atom Count: 18933 
• Modelled Residue Count: 2356 
• Deposited Residue Count: 2920 
• Unique protein chains: 1

6B5V

Structure of TRPV5 in complex with econazole

• DOI: 10.2210/pdb6B5V/pdb
• EMDataResource: EMD-7058

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2017-09-29 Released: 2017-12-27 
• Deposition Author(s): Hughes, T.E.T., Lodowski, D.T., Huynh, K.W., Yazici, A., del Rosario, J., Kapoor, A., Basak, S., Samanta, A., Chakrapani, S., Zhou, Z.H., Filizola, M., Rohacs, T., Han, S., Moiseenkova-Bell, V.Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 29323279 
• 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. 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.

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Organizational Affiliation: 

Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transient receptor potential cation channel subfamily V member 5	A, B, C, D	730	Oryctolagus cuniculus	Mutation(s): 0  Gene Names: Trpv5, Ecac1
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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ECL	A, B, C, D	1-[(2R)-2-[(4-chlorobenzyl)oxy]-2-(2,4-dichlorophenyl)ethyl]-1H-imidazole C18 H15 Cl3 N2 O LEZWWPYKPKIXLL-SFHVURJKSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-09-29 
• Released Date: 2017-12-27 
Deposition Author(s): Hughes, T.E.T., Lodowski, D.T., Huynh, K.W., Yazici, A., del Rosario, J., Kapoor, A., Basak, S., Samanta, A., Chakrapani, S., Zhou, Z.H., Filizola, M., Rohacs, T., Han, S., Moiseenkova-Bell, V.Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	NIGMS 1R01GM103899-01A1

Revision History  

• 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