5X9Z

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.31 Å
  • R-Value Free: 0.394 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.321 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1073/pnas.1701420114

  • PubMed Abstract: 

    The inositol 1,4,5-trisphosphate (IP 3 ) receptor (IP 3 R) is an IP 3 -gated ion channel that releases calcium ions (Ca 2+ ) from the endoplasmic reticulum. The IP 3 -binding sites in the large cytosolic domain are distant from the Ca 2+ conducting pore, and the allosteric mechanism of how IP 3 opens the Ca 2+ 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 IP 3 R in the absence and presence of IP 3 Analyses of two distinct space group crystals uncovered an IP 3 -dependent global translocation of the curvature α-helical domain interfacing with the cytosolic and channel domains. Mutagenesis of the IP 3 R channel revealed an essential role of a leaflet structure in the α-helical domain. These results suggest that the curvature α-helical domain relays IP 3 -controlled global conformational dynamics to the channel through the leaflet, conferring long-range allosteric coupling from IP 3 binding to the Ca 2+ channel.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol 1,4,5-trisphosphate receptor type 1
A, B
2,217Mus musculusMutation(s): 0 
Gene Names: Itpr1Insp3rPcd6Pcp1
UniProt & NIH Common Fund Data Resources
Find proteins for P11881 (Mus musculus)
Explore P11881 
Go to UniProtKB:  P11881
IMPC:  MGI:96623
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11881
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7.31 Å
  • R-Value Free: 0.394 
  • R-Value Work: 0.317 
  • R-Value Observed: 0.321 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.503α = 90
b = 221.726β = 90
c = 318.452γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan15K06791

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-05-17
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description