1N4K | pdb_00001n4k

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.248 (Depositor) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.224 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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:  
    1N4K

  • 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.

Macromolecules
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3P
Query on I3P

Download Ideal Coordinates CCD File 
B [auth A]D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
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)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.248 (Depositor) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.224 (Depositor) 
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
CNSrefinement
CNSphasing

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