3W9G

Crystal structure of the ankyrin repeat domain of chicken TRPV4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P2

Takahashi, N.Hamada-Nakahara, S.Itoh, Y.Takemura, K.Shimada, A.Ueda, Y.Kitamata, M.Matsuoka, R.Hanawa-Suetsugu, K.Senju, Y.Mori, M.X.Kiyonaka, S.Kohda, D.Kitao, A.Mori, Y.Suetsugu, S.

(2014) Nat Commun 5: 4994-4994

  • DOI: https://doi.org/10.1038/ncomms5994
  • Primary Citation of Related Structures:  
    3W9F, 3W9G

  • PubMed Abstract: 

    Mutations in the ankyrin repeat domain (ARD) of TRPV4 are responsible for several channelopathies, including Charcot-Marie-Tooth disease type 2C and congenital distal and scapuloperoneal spinal muscular atrophy. However, the molecular pathogenesis mediated by these mutations remains elusive, mainly due to limited understanding of the TRPV4 ARD function. Here we show that phosphoinositide binding to the TRPV4 ARD leads to suppression of the channel activity. Among the phosphoinositides, phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) most potently binds to the TRPV4 ARD. The crystal structure of the TRPV4 ARD in complex with inositol-1,4,5-trisphosphate, the head-group of PI(4,5)P2, and the molecular-dynamics simulations revealed the PI(4,5)P2-binding amino-acid residues. The TRPV4 channel activities were increased by titration or hydrolysis of membrane PI(4,5)P2. Notably, disease-associated TRPV4 mutations that cause a gain-of-function phenotype abolished PI(4,5)P2 binding and PI(4,5)P2 sensitivity. These findings identify TRPV4 ARD as a lipid-binding domain in which interactions with PI(4,5)P2 normalize the channel activity in TRPV4.


  • Organizational Affiliation

    1] Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, and Laboratory of Environmental Systems Biology, Department of Technology and Ecology, Hall of Global Environmental Studies, Kyoto University, Kyoto 615-8510, Japan [2] Advanced Biomedical Engineering Research Unit, Kyoto University, Kyoto 615-8510, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vanilloid receptor-related osmotically activated channel protein
A, B, C, D
260Gallus gallusMutation(s): 0 
Gene Names: TRPV4VR-OAC
UniProt
Find proteins for A0A1D5PXA5 (Gallus gallus)
Explore A0A1D5PXA5 
Go to UniProtKB:  A0A1D5PXA5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D5PXA5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.952α = 90
b = 48.267β = 101.79
c = 134.029γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description