5XA1 | pdb_00005xa1

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

• PDB DOI: https://doi.org/10.2210/pdb5XA1/pdb

• Classification: METAL TRANSPORT
• Organism(s): Mus musculus
• Expression System: Spodoptera
• Mutation(s): No 


• Deposited: 2017-03-10 Released: 2017-04-19 
• Deposition Author(s): Hamada, K., Miyatake, H., Terauchi, A., Mikoshiba, K.
• Funding Organization(s): JSPS

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.20 Å
• R-Value Free: 
  0.382 (Depositor), 0.390 (DCC) 
• R-Value Work: 
  0.360 (Depositor), 0.352 (DCC) 
• R-Value Observed: 
  0.361 (Depositor) 

Starting Models: experimental

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

• PubMed: 28416699 
• DOI: https://doi.org/10.1073/pnas.1701420114
• Primary Citation Related Structures: 
  5GUG, 5X9Z, 5XA0, 5XA1


• 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.

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Organizational Affiliation: 
• Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, Saitama 351-0198, Japan.
Nano Medical Engineering Laboratory, RIKEN, Saitama 351-0198, Japan.
Laboratory for Developmental Neurobiology, Brain Science Institute, RIKEN, Saitama 351-0198, Japan; [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 362.86 kDa 
• Atom Count: 15,198 
• Modeled Residue Count: 2,514 
• Deposited Residue Count: 3,162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol 1,4,5-trisphosphate receptor type 1	A, B	1,581	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
I3P	C [auth A], D [auth B]	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE C6 H15 O15 P3 MMWCIQZXVOZEGG-XJTPDSDZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I3P	BindingDB:  5XA1	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: 6.20 Å
• R-Value Free:  0.382 (Depositor), 0.390 (DCC) 
• R-Value Work:  0.360 (Depositor), 0.352 (DCC) 
• R-Value Observed: 0.361 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.803	α = 90
b = 126.803	β = 90
c = 367.784	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Hamada, K., Miyatake, H., Terauchi, A., Mikoshiba, K.

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Funding Organization	Location	Grant Number
JSPS	Japan	15K06791

Revision History  

• 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