1N4K

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 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nature01268
  • Structures With Same Primary Citation

  • 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 human ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inositol 1,4,5-trisphosphate receptor type 1A381Mus musculusMutation(s): 0 
Gene Names: ITPR1 OR INSP3RItpr1Insp3rPcd6Pcp1
Find proteins for P11881 (Mus musculus)
Explore P11881 
Go to UniProtKB:  P11881
NIH Common Fund Data Resources
IMPC  MGI:96623
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3P
Query on I3P

Download CCD File 
A
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I3PKd :  0.09000000357627869   nM  PDBBind
I3PKd:  12.5   nM  BindingDB
I3PEC50:  24.799999237060547   nM  BindingDB
I3PKd:  0.09000000357627869   nM  Binding MOAD
I3PKd:  0.20999999344348907   nM  BindingDB
I3PKd:  2.319999933242798   nM  BindingDB
I3PIC50:  300   nM  BindingDB
I3PEC50:  20   nM  BindingDB
I3PEC50:  23   nM  BindingDB
I3PKd:  260   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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