Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126.80 kDa 
• Atom Count: 7823 
• Residue Count: 977 
• Unique protein chains: 1

2E4Y

Crystal structure of the extracellular region of the group II metabotropic glutamate receptor complexed with 2R,4R-APDC

• DOI: 10.2210/pdb2E4Y/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2006-12-17 Released: 2007-02-27 
• Deposition Author(s): Muto, T., Tsuchiya, D., Morikawa, K., Jingami, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 

Literature

Structures of the extracellular regions of the group II/III metabotropic glutamate receptors

Muto, T., Tsuchiya, D., Morikawa, K., Jingami, H.

(2007) Proc Natl Acad Sci U S A 104: 3759-3764

• PubMed: 17360426 
• DOI: 10.1073/pnas.0611577104
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Metabotropic glutamate receptors play major roles in the activation of excitatory synapses in the central nerve system. We determined the crystal structure of the entire extracellular region of the group II receptor and that of the ligand-binding region of the group III receptor. A comparison among groups I, II, and III provides the structural basis that could account for the discrimination of group-specific agonists. Furthermore, the structure of group II includes the cysteine-rich domain, which is tightly linked to the ligand-binding domain by a disulfide bridge, suggesting a potential role in transmitting a ligand-induced conformational change into the downstream transmembrane region. The structure also reveals the lateral interaction between the two cysteine-rich domains, which could stimulate clustering of the dimeric receptors on the cell surface. We propose a general activation mechanism of the dimeric receptor coupled with both ligand-binding and interprotomer rearrangements.

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Organizational Affiliation: 

Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Metabotropic glutamate receptor 3	A, B	555	Rattus norvegicus	Mutation(s): 2  Gene Names: Grm3, Gprc1c, Mglur3
Find proteins for P31422 (Rattus norvegicus) Go to UniProtKB:  P31422

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
52A	A, B	(2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid C6 H10 N2 O4 XZFMJVJDSYRWDQ-AWFVSMACSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
52A	Ki:  410   nM  BindingDB
52A	EC50:  1700   nM  BindingDB
52A	EC50:  3000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.228 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.393	α = 90
b = 91.799	β = 92.28
c = 112.972	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-12-17 
• Released Date: 2007-02-27 
Deposition Author(s): Muto, T., Tsuchiya, D., Morikawa, K., Jingami, H.

Revision History 

• Version 1.0: 2007-02-27
  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