2E4Y

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

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 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


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

  • DOI: 10.1073/pnas.0611577104
  • Primary Citation of Related Structures:  
    2E4U, 2E4V, 2E4W, 2E4X, 2E4Y, 2E4Z

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metabotropic glutamate receptor 3A, B555Rattus norvegicusMutation(s): 2 
Gene Names: Grm3, Gprc1c, Mglur3
UniProt
Find proteins for P31422 (Rattus norvegicus)
Explore P31422 
Go to UniProtKB:  P31422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31422
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
52A
Query on 52A
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		(2R,4R)-4-aminopyrrolidine-2,4-dicarboxylic acid
C6 H10 N2 O4
XZFMJVJDSYRWDQ-AWFVSMACSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
52A BindingDB:  2E4Y Ki: 410 (nM) from 1 assay(s)
EC50: min: 1700, max: 3000 (nM) from 2 assay(s)
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 = 84.393α = 90
b = 91.799β = 92.28
c = 112.972γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-11-10
    Changes: Advisory, Database references, Structure summary