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- PDB-1iss: Crystal Structure of Metabotropic Glutamate Receptor Subtype 1 Co... -

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Basic information

Entry
Database: PDB / ID: 1iss
TitleCrystal Structure of Metabotropic Glutamate Receptor Subtype 1 Complexed with an antagonist
ComponentsMetabotropic Glutamate Receptor subtype 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / NEUROTRANSMITTER / G PROTEIN COUPLED RECEPTOR / ANTAGONIST / 4-CARBOXYPHENYLGLYCINE
Function / homology
Function and homology information


PLC activating G protein-coupled glutamate receptor activity / dendriole / 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) / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / Neurexins and neuroligins ...PLC activating G protein-coupled glutamate receptor activity / dendriole / 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) / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / synaptic signaling via neuropeptide / Neurexins and neuroligins / cellular response to electrical stimulus / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / regulation of sensory perception of pain / L-glutamate import across plasma membrane / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / G alpha (q) signalling events / regulation of glutamate secretion / synaptic transmission, GABAergic / membrane depolarization / regulation of synaptic transmission, glutamatergic / sensory perception of pain / nuclear estrogen receptor binding / locomotory behavior / calcium-mediated signaling / G protein-coupled receptor activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / positive regulation of MAPK cascade / postsynaptic density / G protein-coupled receptor signaling pathway / axon / neuronal cell body / 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 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain ...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 3. / 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 / 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
(S)-(ALPHA)-METHYL-4-CARBOXYPHENYLGLYCINE / Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTsuchiya, D. / Kunishima, N. / Kamiya, N. / Jingami, H. / Morikawa, K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+.
Authors: Tsuchiya, D. / Kunishima, N. / Kamiya, N. / Jingami, H. / Morikawa, K.
#1: Journal: 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
DepositionDec 21, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)110,9364
Polymers110,5172
Non-polymers4182
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.142, 112.142, 289.905
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


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) / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P23385
#2: Chemical ChemComp-MCG / (S)-(ALPHA)-METHYL-4-CARBOXYPHENYLGLYCINE / 4-(1-AMINO-1-CARBOXY-ETHYL)-BENZOIC ACID


Type: L-peptide linking / Mass: 209.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11NO4
Has protein modificationY

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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: 4.12 Å3/Da / Density % sol: 70.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: AMMONIUM SULFATE, TRIS-HCl, MCPG, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Kunishima, N., (2000) Nature, 407, 971.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 MTris-HCl1reservoirpH8.5
21.9 Mammonium sulfate1reservoir
310 mMS-MCPG1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.836 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 1, 2000
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.836 Å / Relative weight: 1
ReflectionResolution: 3.3→20 Å / Num. all: 27580 / Num. obs: 27580 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 79.2 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 3.3→3.37 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1739 / % possible all: 99.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A of PDB ENTRY 1EWK

1ewk


Resolution: 3.3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2062 7.92 %RANDOM
Rwork0.257 ---
all-28564 --
obs-26032 91.1 %-
Displacement parametersBiso mean: 64.3 Å2
Baniso -1Baniso -2Baniso -3
1-31.008 Å231.008 Å2-62.016 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.48 Å
Luzzati d res low-0.48 Å
Luzzati sigma a0.96 Å0.85 Å
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 30 0 7124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.0095
X-RAY DIFFRACTIONc_angle_d1.38
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_deg0.949
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.33 Å / Rfactor Rfree: 0.445 / Rfactor Rwork: 0.461

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