1XZZ | pdb_00001xzz

Crystal structure of the ligand binding suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor

• PDB DOI: https://doi.org/10.2210/pdb1XZZ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-11-13 Released: 2005-01-25 
• Deposition Author(s): Bosanac, I., Yamazaki, H., Matsu-ura, T., Michikawa, T., Mikoshiba, K., Ikura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal structure of the ligand binding suppressor domain of type 1 inositol 1,4,5-trisphosphate receptor.

Bosanac, I., Yamazaki, H., Matsu-Ura, T., Michikawa, T., Mikoshiba, K., Ikura, M.

(2005) Mol Cell 17: 193-203

• PubMed: 15664189 
• DOI: https://doi.org/10.1016/j.molcel.2004.11.047
• Primary Citation Related Structures: 
  1XZZ


• PubMed Abstract: 
  

  Binding of inositol 1,4,5-trisphosphate (IP(3)) to the amino-terminal region of IP(3) receptor promotes Ca(2+) release from the endoplasmic reticulum. Within the amino terminus, the first 220 residues directly preceding the IP(3) binding core domain play a key role in IP(3) binding suppression and regulatory protein interaction. Here we present a crystal structure of the suppressor domain of the mouse type 1 IP(3) receptor at 1.8 A. Displaying a shape akin to a hammer, the suppressor region contains a Head subdomain forming the beta-trefoil fold and an Arm subdomain possessing a helix-turn-helix structure. The conserved region on the Head subdomain appeared to interact with the IP(3) binding core domain and is in close proximity to the previously proposed binding sites of Homer, RACK1, calmodulin, and CaBP1. The present study sheds light onto the mechanism underlying the receptor's sensitivity to the ligand and its communication with cellular signaling proteins.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.51 kDa 
• Atom Count: 1,841 
• Modeled Residue Count: 216 
• Deposited Residue Count: 246 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 1,4,5-trisphosphate receptor type 1	A	246	Mus musculus	Mutation(s): 0  Gene Names: Itpr1, Insp3r, Pcd6, Pcp1
UniProt & NIH Common Fund Data Resources
Find proteins for P11881 (Mus musculus) Explore P11881  Go to UniProtKB:  P11881
IMPC:  MGI:96623

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.3	α = 90
b = 147.3	β = 90
c = 65	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Bosanac, I., Yamazaki, H., Matsu-ura, T., Michikawa, T., Mikoshiba, K., Ikura, M.

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations