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

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Basic information

Entry
Database: PDB / ID: 1isr
TitleCrystal Structure of Metabotropic Glutamate Receptor Subtype 1 Complexed with Glutamate and Gadolinium Ion
ComponentsMetabotropic Glutamate Receptor subtype 1
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION / NEUROTRANSMITTER / G PROTEIN COUPLED RECEPTOR / AGONIST / GADOLINIUM ION
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
GADOLINIUM ATOM / GLUTAMIC ACID / Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 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 27, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic Glutamate Receptor subtype 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7204
Polymers55,2591
Non-polymers4623
Water00
1
A: Metabotropic Glutamate Receptor subtype 1
hetero molecules

A: Metabotropic Glutamate Receptor subtype 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4418
Polymers110,5172
Non-polymers9236
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+4/31
Unit cell
Length a, b, c (Å)145.348, 145.348, 76.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2002-

GD

DetailsThe biological dimer is generated by the two fold axis: x-y,-y,4/3-z

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Components

#1: Protein Metabotropic Glutamate Receptor subtype 1


Mass: 55258.707 Da / Num. of mol.: 1 / 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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, HEPES, L-glutamate, gadolinium chloride, pH 7.5, 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-IDDetailsChemical formula
10.2 MHEPES1reservoirpH7.5
220 %PEG40001reservoir
31 mML-glutamate1reservoir
40.5 mM1reservoirGdCl3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL40B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. all: 5935 / Num. obs: 5935 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 41.4 Å2 / Rmerge(I) obs: 0.101
Reflection shellResolution: 4→4.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / Num. unique all: 440 / % possible all: 90.1
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 4 Å / Lowest resolution: 4.2 Å / % possible obs: 75.6 % / Rmerge(I) obs: 0.23

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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: 4→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 552 7.69 %RANDOM
Rwork0.237 ---
all0.238 7182 --
obs0.238 7182 89.3 %-
Displacement parametersBiso mean: 62.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.142 Å2-9.935 Å20 Å2
2---2.142 Å20 Å2
3---4.284 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.46 Å
Luzzati d res low-0.46 Å
Luzzati sigma a0.63 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 12 0 3572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.925
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_deg0.62
LS refinement shellResolution: 4→4.13 Å
RfactorNum. reflection% reflection
Rfree0.332 57 -
Rwork0.277 --
obs-527 81.6 %
Refinement
*PLUS
Highest resolution: 4 Å / Lowest resolution: 12 Å / % reflection Rfree: 7 % / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.003
LS refinement shell
*PLUS
Rfactor obs: 0.277

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