1ISR

Crystal Structure of Metabotropic Glutamate Receptor Subtype 1 Complexed with Glutamate and Gadolinium Ion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 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 crystal ...

    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.


    Related Citations: 
    • Structural Basis of Glutamate Recognition by a Dimeric Metabotropic Glutamate Receptor
      Kunishima, N., Shimada, Y., Tsuji, Y., Sato, T., Yamamoto, M., Kumasaka, T., Nakanishi, S., Jingami, H., Morikawa, K.
      (2000) Nature 407: 971

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Metabotropic Glutamate Receptor subtype 1A490Rattus norvegicusMutation(s): 0 
Gene Names: Grm1Gprc1aMglur1
Find proteins for P23385 (Rattus norvegicus)
Explore P23385 
Go to UniProtKB:  P23385
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download CCD File 
A
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GGLEC50:  9000   nM  BindingDB
GGLEC50:  7300   nM  BindingDB
GGLEC50:  13000   nM  BindingDB
GGLEC50:  19000   nM  BindingDB
GGLEC50:  13870   nM  BindingDB
GGLEC50:  56000   nM  BindingDB
GGLEC50:  1050   nM  BindingDB
GGLKi:  570   nM  BindingDB
GGLKi:  9000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
GGLEC50:  3000   nM  BindingDB
GGLEC50:  12000   nM  BindingDB
GGLEC50:  1600   nM  BindingDB
GGLKi:  250   nM  BindingDB
GGLEC50:  1585   nM  BindingDB
GGLEC50:  156000   nM  BindingDB
GGLKi:  10000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.348α = 90
b = 145.348β = 90
c = 76.754γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance