1EWK | pdb_00001ewk

CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 COMPLEXED WITH GLUTAMATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

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: 971-977

  • DOI: https://doi.org/10.1038/35039564
  • Primary Citation Related Structures: 
    1EWK, 1EWT, 1EWV

  • PubMed Abstract: 

    The metabotropic glutamate receptors (mGluRs) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. Here we have determined three different crystal structures of the extracellular ligand-binding region of mGluR1--in a complex with glutamate and in two unliganded forms. They all showed disulphide-linked homodimers, whose 'active' and 'resting' conformations are modulated through the dimeric interface by a packed alpha-helical structure. The bi-lobed protomer architectures flexibly change their domain arrangements to form an 'open' or 'closed' conformation. The structures imply that glutamate binding stabilizes both the 'active' dimer and the 'closed' protomer in dynamic equilibrium. Movements of the four domains in the dimer are likely to affect the separation of the transmembrane and intracellular regions, and thereby activate the receptor. This scheme in the initial receptor activation could be applied generally to G-protein-coupled neurotransmitter receptors that possess extracellular ligand-binding sites.


  • Organizational Affiliation
    • Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka, Japan.

Macromolecule Content 

  • Total Structure Weight: 112.46 kDa 
  • Atom Count: 7,906 
  • Modeled Residue Count: 897 
  • Deposited Residue Count: 980 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
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
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P23385-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B],
M [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU

Query on GLU



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.375α = 90
b = 95.219β = 114.85
c = 97.451γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary