5X9Z

Crystal structure of inositol 1,4,5-trisphosphate receptor large cytosolic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.311 Å
  • R-Value Free: 0.394 
  • R-Value Work: 0.317 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

IP3-mediated gating mechanism of the IP3 receptor revealed by mutagenesis and X-ray crystallography

Hamada, K.Miyatake, H.Terauchi, A.Mikoshiba, K.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 4661-4666

  • DOI: 10.1073/pnas.1701420114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and th ...

    The inositol 1,4,5-trisphosphate (IP3) receptor (IP3R) is an IP3-gated ion channel that releases calcium ions (Ca2+) from the endoplasmic reticulum. The IP3-binding sites in the large cytosolic domain are distant from the Ca2+ conducting pore, and the allosteric mechanism of how IP3 opens the Ca2+ channel remains elusive. Here, we identify a long-range gating mechanism uncovered by channel mutagenesis and X-ray crystallography of the large cytosolic domain of mouse type 1 IP3R in the absence and presence of IP3 Analyses of two distinct space group crystals uncovered an IP3-dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP3R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP3-controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP3 binding to the Ca2+ channel.


    Organizational Affiliation

    Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, Saitama 351-0198, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol 1,4,5-trisphosphate receptor type 1
A, B
2217Mus musculusMutation(s): 0 
Gene Names: Itpr1 (Insp3r, Pcd6, Pcp1)
Find proteins for P11881 (Mus musculus)
Go to UniProtKB:  P11881
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.311 Å
  • R-Value Free: 0.394 
  • R-Value Work: 0.317 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 212.503α = 90.00
b = 221.726β = 90.00
c = 318.452γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan15K06791

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references