1ISS

Crystal Structure of Metabotropic Glutamate Receptor Subtype 1 Complexed with an antagonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.257 

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This is version 1.3 of the entry. See complete history


Literature

Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+.

Tsuchiya, D.Kunishima, N.Kamiya, N.Jingami, H.Morikawa, K.

(2002) Proc Natl Acad Sci U S A 99: 2660-2665

  • DOI: https://doi.org/10.1073/pnas.052708599
  • Primary Citation of Related Structures:  
    1ISR, 1ISS

  • PubMed Abstract: 

    Crystal structures of the extracellular ligand-binding region of the metabotropic glutamate receptor, complexed with an antagonist, (S)-(alpha)-methyl-4-carboxyphenylglycine, and with both glutamate and Gd3+ ion, have been determined by x-ray crystallographic analyses. The structure of the complex with the antagonist is similar to that of the unliganded resting dimer. The antagonist wedges the protomer to maintain an inactive open form. The glutamate/Gd3+ complex is an exact 2-fold symmetric dimer, where each bi-lobed protomer adopts the closed conformation. The surface of the C-terminal domain contains an acidic patch, whose negative charges are alleviated by the metal cation to stabilize the active dimeric structure. The structural comparison between the active and resting dimers suggests that glutamate binding tends to induce domain closing and a small shift of a helix in the dimer interface. Furthermore, an interprotomer contact including the acidic patch inhibited dimer formation by the two open protomers in the active state. These findings provide a structural basis to describe the link between ligand binding and the dimer interface.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metabotropic Glutamate Receptor subtype 1
A, B
490Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P23385 (Rattus norvegicus)
Explore P23385 
Go to UniProtKB:  P23385
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23385
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MCG
Query on MCG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(S)-(ALPHA)-METHYL-4-CARBOXYPHENYLGLYCINE
C10 H11 N O4
DNCAZYRLRMTVSF-JTQLQIEISA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MCG BindingDB:  1ISS Ki: min: 165, max: 5.40e+5 (nM) from 5 assay(s)
IC50: min: 4300, max: 7.00e+5 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.257 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.142α = 90
b = 112.142β = 90
c = 289.905γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description