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 1.4 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: https://doi.org/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.


  • Organizational Affiliation

    Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 5A,
B,
C [auth D],
D [auth C]
730Oryctolagus cuniculusMutation(s): 0 
Gene Names: Trpv5Ecac1
Membrane Entity: Yes 
UniProt
Find proteins for Q9XSM3 (Oryctolagus cuniculus)
Explore Q9XSM3 
Go to UniProtKB:  Q9XSM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XSM3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.12rc0
RECONSTRUCTIONRELION2.0

Structure Validation

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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
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references