6PBF

ZINC9155420-bound TRPV5 in nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

Structure-based characterization of novel TRPV5 inhibitors.

Hughes, T.E.Del Rosario, J.S.Kapoor, A.Yazici, A.T.Yudin, Y.Fluck, E.C.Filizola, M.Rohacs, T.Moiseenkova-Bell, V.Y.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.49572
  • Primary Citation of Related Structures:  
    6PBE, 6PBF

  • PubMed Abstract: 

    Transient receptor potential vanilloid 5 (TRPV5) is a highly calcium selective ion channel that acts as the rate-limiting step of calcium reabsorption in the kidney. The lack of potent, specific modulators of TRPV5 has limited the ability to probe the contribution of TRPV5 in disease phenotypes such as hypercalcemia and nephrolithiasis. Here, we performed structure-based virtual screening (SBVS) at a previously identified TRPV5 inhibitor binding site coupled with electrophysiology screening and identified three novel inhibitors of TRPV5, one of which exhibits high affinity, and specificity for TRPV5 over other TRP channels, including its close homologue TRPV6. Cryo-electron microscopy of TRPV5 in the presence of the specific inhibitor and its parent compound revealed novel binding sites for this channel. Structural and functional analysis have allowed us to suggest a mechanism of action for the selective inhibition of TRPV5 and lay the groundwork for rational design of new classes of TRPV5 modulators.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily V member 5
A, B, C, D
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: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

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 StatesR01GM103899
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM129357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093290

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references