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- PDB-4xas: mGluR2 ECD ligand complex -

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Basic information

Entry
Database: PDB / ID: 4xas
TitlemGluR2 ECD ligand complex
ComponentsMetabotropic glutamate receptor 2
KeywordsSIGNALING PROTEIN / mGluR2 ECD
Function / homology
Function and homology information


regulation of response to drug / group II metabotropic glutamate receptor activity / behavioral response to nicotine / G protein-coupled glutamate receptor signaling pathway / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate secretion / glutamate receptor activity ...regulation of response to drug / group II metabotropic glutamate receptor activity / behavioral response to nicotine / G protein-coupled glutamate receptor signaling pathway / intracellular glutamate homeostasis / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate secretion / glutamate receptor activity / regulation of glutamate secretion / long-term synaptic depression / regulation of dopamine secretion / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / presynaptic modulation of chemical synaptic transmission / response to cocaine / G protein-coupled receptor activity / presynaptic membrane / gene expression / G alpha (i) signalling events / scaffold protein binding / chemical synaptic transmission / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / axon / glutamatergic synapse / dendrite / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 2 / 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, metabotropic glutamate receptor 2 / 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
Chem-40H / Metabotropic glutamate receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 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 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 2
B: Metabotropic glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8484
Polymers111,4262
Non-polymers4222
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-5 kcal/mol
Surface area35830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.044, 135.858, 92.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Metabotropic glutamate receptor 2 / / mGluR2


Mass: 55712.832 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-493
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM2, GPRC1B, MGLUR2 / Production host: unidentified baculovirus / References: UniProt: Q14416
#2: Chemical ChemComp-40H / (1R,4S,5S,6S)-4-aminospiro[bicyclo[3.1.0]hexane-2,1'-cyclopropane]-4,6-dicarboxylic acid


Mass: 211.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 100mM Sodium Acetate pH 4.6 + 23% PEG 10K

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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: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.35→19.7 Å / Num. obs: 40851 / % possible obs: 98.5 % / Redundancy: 6.1 % / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
SCALAdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementResolution: 2.35→19.7 Å / Cor.coef. Fo:Fc: 0.8753 / Cor.coef. Fo:Fc free: 0.8124 / SU R Cruickshank DPI: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.275
RfactorNum. reflection% reflectionSelection details
Rfree0.2801 1653 4.05 %RANDOM
Rwork0.2116 ---
obs0.2144 40851 98.45 %-
Displacement parametersBiso max: 150.27 Å2 / Biso mean: 48.95 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-11.74 Å20 Å20 Å2
2---23.0352 Å20 Å2
3---11.2952 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: final / Resolution: 2.35→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6830 0 30 207 7067
Biso mean--33.78 44.44 -
Num. residues----878
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2358SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1059HARMONIC5
X-RAY DIFFRACTIONt_it7036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion897SEMIHARMONIC5
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_contact8335SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7036HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9570HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.55
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3274 107 3.74 %
Rwork0.244 2753 -
all0.247 2860 -
obs--98.45 %

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