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

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Basic information

Entry
Database: PDB / ID: 1ewt
TitleCRYSTAL STRUCTURE OF METABOTROPIC GLUTAMATE RECEPTOR SUBTYPE 1 LIGAND FREE FORM I
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 / G protein-coupled receptor homodimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / 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 / G protein-coupled receptor homodimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / 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 / chemical synaptic transmission, postsynaptic / regulation of postsynaptic cytosolic calcium ion concentration / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / glutamate receptor activity / G alpha (q) signalling events / synaptic transmission, GABAergic / regulation of glutamate secretion / membrane depolarization / sensory perception of pain / regulation of synaptic transmission, glutamatergic / 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 / dendritic spine / postsynaptic density / positive regulation of MAPK cascade / neuron projection / G protein-coupled receptor signaling pathway / axon / dendrite / glutamatergic synapse / 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 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / 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: 3.7 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: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)111,1237
Polymers110,5172
Non-polymers6055
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.436, 111.436, 293.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 4.23 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: AMMONIUM SULFATE, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.9 Mammonium sulfate1drop
210 mg/mlprotein1drop
3200 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: 3.7→12 Å / Num. all: 119429 / Num. obs: 19643 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.08 % / Biso Wilson estimate: 84.2 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 11.6
Reflection shellResolution: 3.7→3.83 Å / % possible obs: 100 % / Redundancy: 5.96 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3023 / % possible all: 100
Reflection
*PLUS
Num. measured all: 119429

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Processing

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

1ewk


Resolution: 3.7→12 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 950 4.8 %RANDOM
Rwork0.244 ---
all-119429 --
obs-19643 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.7739 Å2 / ksol: 0.27754 e/Å3
Displacement parametersBiso mean: 72 Å2
Baniso -1Baniso -2Baniso -3
1--18.13 Å20 Å20 Å2
2---18.13 Å20 Å2
3---36.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7248 0 34 0 7282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.05
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: 3.7→3.92 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6 / Redundancy reflection obs: 3.5
RfactorNum. reflection% reflection
Rfree0.311 134 4.4 %
Rwork0.281 2889 -
obs--93.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.7 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 72 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
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
Rfactor Rfree: 0.311 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.281

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