Crystal structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with IP3

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structure of the inositol 1,4,5-trisphosphate receptor binding core in complex with its ligand.

Bosanac, I.Alattia, J.R.Mal, T.K.Chan, J.Talarico, S.Tong, F.K.Tong, K.I.Yoshikawa, F.Furuichi, T.Iwai, M.Michikawa, T.Mikoshiba, K.Ikura, M.

(2002) Nature 420: 696-700

  • DOI: https://doi.org/10.1038/nature01268
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In a variety of cells, the Ca2+ signalling process is mediated by the endoplasmic-reticulum-membrane-associated Ca2+ release channel, inositol 1,4,5-trisphosphate (InsP3) receptor (InsP3R). Being ubiquitous and present in organisms ranging from humans to Caenorhabditis elegans, InsP3R has a vital role in the control of cellular and physiological processes as diverse as cell division, cell proliferation, apoptosis, fertilization, development, behaviour, memory and learning. Mouse type I InsP3R (InsP3R1), found in high abundance in cerebellar Purkinje cells, is a polypeptide with three major functionally distinct regions: the amino-terminal InsP3-binding region, the central modulatory region and the carboxy-terminal channel region. Here we present a 2.2-A crystal structure of the InsP3-binding core of mouse InsP3R1 in complex with InsP3. The asymmetric, boomerang-like structure consists of an N-terminal beta-trefoil domain and a C-terminal alpha-helical domain containing an 'armadillo repeat'-like fold. The cleft formed by the two domains exposes a cluster of arginine and lysine residues that coordinate the three phosphoryl groups of InsP3. Putative Ca2+-binding sites are identified in two separate locations within the InsP3-binding core.

  • Organizational Affiliation

    Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ontario, Canada M5G 2M9.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol 1,4,5-trisphosphate receptor type 1381Mus musculusMutation(s): 0 
Gene Names: ITPR1 OR INSP3R
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on I3P

Download Ideal Coordinates CCD File 
C6 H15 O15 P3
Binding Affinity Annotations 
IDSourceBinding Affinity
I3P BindingDB:  1N4K Kd: min: 0.21, max: 260 (nM) from 5 assay(s)
IC50: 300 (nM) from 1 assay(s)
EC50: min: 20, max: 209 (nM) from 7 assay(s)
PDBBind:  1N4K Kd: 0.09 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.101α = 90
b = 90.42β = 90
c = 207.117γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations