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- PDB-4xar: mGluR2 ECD and mGluR3 ECD complex with ligands -

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Basic information

Entry
Database: PDB / ID: 4xar
TitlemGluR2 ECD and mGluR3 ECD complex with ligands
ComponentsMetabotropic glutamate receptor 3
KeywordsSIGNALING PROTEIN / mGluR2 mGluR3 ECD
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / negative regulation of adenylate cyclase activity / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity ...group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / negative regulation of adenylate cyclase activity / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / cellular response to stress / postsynaptic modulation of chemical synaptic transmission / regulation of synaptic transmission, glutamatergic / calcium channel regulator activity / G protein-coupled receptor activity / presynaptic membrane / scaffold protein binding / G alpha (i) signalling events / gene expression / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynaptic density / axon / glutamatergic synapse / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 3 / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site ...GPCR, family 3, metabotropic glutamate receptor 3 / 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 / G-protein coupled receptors family 3 signature 3. / 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
Chem-40F / IODIDE ION / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsClawson, D.K.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Synthesis and Pharmacological Characterization of C4-Disubstituted Analogs of 1S,2S,5R,6S-2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylate: Identification of a Potent, Selective Metabotropic ...Title: Synthesis and Pharmacological Characterization of C4-Disubstituted Analogs of 1S,2S,5R,6S-2-Aminobicyclo[3.1.0]hexane-2,6-dicarboxylate: Identification of a Potent, Selective Metabotropic Glutamate Receptor Agonist and Determination of Agonist-Bound Human mGlu2 and mGlu3 Amino Terminal Domain Structures.
Authors: Monn, J.A. / Prieto, L. / Taboada, L. / Pedregal, C. / Hao, J. / Reinhard, M.R. / Henry, S.S. / Goldsmith, P.J. / Beadle, C.D. / Walton, L. / Man, T. / Rudyk, H. / Clark, B. / Tupper, D. / ...Authors: Monn, J.A. / Prieto, L. / Taboada, L. / Pedregal, C. / Hao, J. / Reinhard, M.R. / Henry, S.S. / Goldsmith, P.J. / Beadle, C.D. / Walton, L. / Man, T. / Rudyk, H. / Clark, B. / Tupper, D. / Baker, S.R. / Lamas, C. / Montero, C. / Marcos, A. / Blanco, J. / Bures, M. / Clawson, D.K. / Atwell, S. / Lu, F. / Wang, J. / Russell, M. / Heinz, B.A. / Wang, X. / Carter, J.H. / Xiang, C. / Catlow, J.T. / Swanson, S. / Sanger, H. / Broad, L.M. / Johnson, M.P. / Knopp, K.L. / Simmons, R.M. / Johnson, B.G. / Shaw, D.B. / McKinzie, D.L.
History
DepositionDec 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,97710
Polymers58,7771
Non-polymers1,2009
Water2,000111
1
A: Metabotropic glutamate receptor 3
hetero molecules

A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95420
Polymers117,5532
Non-polymers2,40118
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4110 Å2
ΔGint-8 kcal/mol
Surface area38350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.338, 80.338, 155.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Metabotropic glutamate receptor 3 / mGluR3


Mass: 58776.562 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM3, GPRC1C, MGLUR3 / Production host: unidentified baculovirus / References: UniProt: Q14832
#2: Chemical ChemComp-40F / (1S,2S,5R,6S)-2-aminobicyclo[3.1.0]hexane-2,6-dicarboxylic acid


Mass: 185.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11NO4
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 20% PEG 3350, 200mM Ammonium Iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.26→37.68 Å / Num. obs: 27749 / % possible obs: 99 % / Redundancy: 10.8 % / Net I/σ(I): 8.2

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.5refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→37.68 Å / Cor.coef. Fo:Fc: 0.9341 / Cor.coef. Fo:Fc free: 0.9253 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.237 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 1135 4.09 %RANDOM
Rwork0.1967 ---
obs0.1979 27749 99.25 %-
Displacement parametersBiso max: 119.13 Å2 / Biso mean: 46.56 Å2 / Biso min: 19.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.7205 Å20 Å20 Å2
2--1.7205 Å20 Å2
3----3.441 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: final / Resolution: 2.26→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 21 111 3658
Biso mean--37.19 47.31 -
Num. residues----445
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1265SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes526HARMONIC5
X-RAY DIFFRACTIONt_it3614HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4163SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3614HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4890HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion17.8
LS refinement shellResolution: 2.26→2.35 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2255 110 3.9 %
Rwork0.2152 2711 -
all0.2156 2821 -
obs--99.25 %

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