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- PDB-1ewv: CRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 LI... -

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Basic information

Entry
Database: PDB / ID: 1ewv
TitleCRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 LIGAND FREE FORM II
ComponentsMETABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / NEUROTRANSMITTER / CNS / NEURON
Function / homology
Function and homology information


PLC activating G protein-coupled glutamate receptor activity / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / Neurexins and neuroligins / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus ...PLC activating G protein-coupled glutamate receptor activity / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / Neurexins and neuroligins / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / L-glutamate import across plasma membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled glutamate receptor signaling pathway / synaptic transmission, GABAergic / glutamate receptor activity / G alpha (q) signalling events / regulation of glutamate secretion / membrane depolarization / regulation of synaptic transmission, glutamatergic / sensory perception of pain / locomotory behavior / G protein-coupled receptor activity / nuclear estrogen receptor binding / calcium-mediated signaling / postsynaptic density membrane / Schaffer collateral - CA1 synapse / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / postsynaptic membrane / positive regulation of MAPK cascade / dendritic spine / postsynaptic density / neuron projection / G protein-coupled receptor signaling pathway / axon / glutamatergic synapse / dendrite / nucleus / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR ...GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / GPCR, family 3, metabotropic glutamate receptor / G-protein coupled receptors family 3 signature 1. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain / GPCR, family 3, nine cysteines domain superfamily / Nine Cysteines Domain of family 3 GPCR / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsKunishima, N. / Shimada, Y. / Tsuji, Y. / Jingami, H. / Morikawa, K.
CitationJournal: Nature / Year: 2000
Title: Structural basis of glutamate recognition by a dimeric metabotropic glutamate receptor.
Authors: Kunishima, N. / Shimada, Y. / Tsuji, Y. / Sato, T. / Yamamoto, M. / Kumasaka, T. / Nakanishi, S. / Jingami, H. / Morikawa, K.
History
DepositionApr 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1
B: METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1


Theoretical massNumber of molelcules
Total (without water)110,5172
Polymers110,5172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.790, 94.530, 95.450
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 / MGLUR1


Mass: 55258.707 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR LIGAND BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line (production host): SF-9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23385

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, AMMONIUM SULFATE, TRIS-HCL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40001drop
210 mg/mlprotein1drop
3100 mMammonium sulfate1drop
4100 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.835
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 14, 1999
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.835 Å / Relative weight: 1
ReflectionResolution: 4→20 Å / Num. all: 26920 / Num. obs: 10557 / % possible obs: 89.1 % / Observed criterion σ(I): -3 / Redundancy: 2.55 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 5.4
Reflection shellResolution: 4→4.14 Å / Redundancy: 2.51 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.6 / % possible all: 77.3
Reflection shell
*PLUS
% possible obs: 77.3 % / Rmerge(I) obs: 0.25

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EWK

1ewk


Resolution: 4→20 Å / Rfactor Rfree error: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.328 534 5.1 %RANDOM
Rwork0.254 ---
all-10557 --
obs-10550 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.258986 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-28.79 Å20 Å219.02 Å2
2---21.73 Å20 Å2
3----7.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7120 0 0 0 7120
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 4→4.25 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 68 4 %
Rwork0.245 1614 -
obs--86.2 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 4 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 35.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 4 Å / Rfactor Rfree: 0.317 / % reflection Rfree: 4 % / Rfactor Rwork: 0.245

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