3T8S | pdb_00003t8s

Apo and InsP3-bound Crystal Structures of the Ligand-Binding Domain of an InsP3 Receptor

• PDB DOI: https://doi.org/10.2210/pdb3T8S/pdb

• Classification: Transport protein, membrane protein
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-01 Released: 2011-09-07 
• Deposition Author(s): Lin, C., Baek, K., Lu, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.77 Å
• R-Value Free: 
  0.292 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.273 (DCC) 
• R-Value Observed: 
  0.278 (Depositor) 

Starting Models: experimental

Literature

Apo and InsP(3)-bound crystal structures of the ligand-binding domain of an InsP(3) receptor.

Lin, C.C., Baek, K., Lu, Z.

(2011) Nat Struct Mol Biol 18: 1172-1174

• PubMed: 21892169 
• DOI: https://doi.org/10.1038/nsmb.2112
• Primary Citation Related Structures: 
  3T8S


• PubMed Abstract: 
  

  We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP(3)R) in its apo and InsP(3)-bound conformations. Comparison of these two conformations reveals that LBD's first β-trefoil fold (β-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second β-trefoil fold (β-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP(3) binding shifts this equilibrium toward the active state.

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Organizational Affiliation: 
• Department of Physiology, Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 132.61 kDa 
• Atom Count: 7,386 
• Modeled Residue Count: 983 
• Deposited Residue Count: 1,170 
• 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	585	Rattus norvegicus	Mutation(s): 0  Gene Names: Insp3r, Itpr1
UniProt
Find proteins for P29994 (Rattus norvegicus) Explore P29994  Go to UniProtKB:  P29994

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
I3P	C [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:  3T8S	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: 3.77 Å
• R-Value Free:  0.292 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.273 (DCC) 
• R-Value Observed: 0.278 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.829	α = 90
b = 84.877	β = 116.92
c = 95.09	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Lin, C., Baek, K., Lu, Z.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Database references
• Version 1.2: 2011-10-26
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description