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- PDB-3sm9: Crystal Structure of Metabotropic glutamate receptor 3 precursor ... -

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Basic information

Entry
Database: PDB / ID: 3sm9
TitleCrystal Structure of Metabotropic glutamate receptor 3 precursor in presence of LY341495 antagonist
ComponentsMetabotropic glutamate receptor 3
KeywordsSIGNALING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / Cell membrane / G-protein coupled receptor / Glycoprotein / Membrane / Olfaction / Phosphoprotein / Receptor / Sensory transduction / Transducer / Transmembrane / Transmembrane helix
Function / homology
Function and homology information


group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity ...group II metabotropic glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / postsynaptic modulation of chemical synaptic transmission / calcium channel regulator activity / regulation of synaptic transmission, glutamatergic / G protein-coupled receptor activity / presynaptic membrane / gene expression / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / 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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...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 / 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-Z99 / Metabotropic glutamate receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsWernimont, A.K. / Dong, A. / Seitova, A. / Crombet, L. / Khutoreskaya, G. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Cossar, D. ...Wernimont, A.K. / Dong, A. / Seitova, A. / Crombet, L. / Khutoreskaya, G. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Cossar, D. / Dobrovetsky, E. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Metabotropic glutamate receptor 3 precursor in presence of LY341495 antagonist
Authors: Wernimont, A.K. / Dong, A. / Seitova, A. / Crombet, L. / Khutoreskaya, G. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Cossar, D. / Dobrovetsky, E.
History
DepositionJun 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4159
Polymers54,5111
Non-polymers9058
Water1,838102
1
A: Metabotropic glutamate receptor 3
hetero molecules

A: Metabotropic glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,83018
Polymers109,0212
Non-polymers1,80916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3370 Å2
ΔGint-178 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.402, 98.633, 203.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Metabotropic glutamate receptor 3 / / mGluR3


Mass: 54510.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPRC1C, GRM3, MGLUR3 / Plasmid: pFHMSP-LIC-C / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14832
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-Z99 / 2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine / (1S,2S)-2-[(2S)-2-amino-1-hydroxy-1-oxo-3-(9H-xanthen-9-yl)propan-2-yl]cyclopropane-1-carboxylic acid / LY-341495


Mass: 353.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO5 / Comment: antidepressant, antagonist*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.84 Å3/Da / Density % sol: 67.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M Ammonium Sulfate 0.1 M BisTris Propane pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 39532 / Num. obs: 39493 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.77 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.25-2.295.60.8762.0819501.37299.8
2.29-2.335.70.7682.5119251.37999.8
2.33-2.385.70.6719491.41899.7
2.38-2.425.70.6119511.36799.9
2.42-2.485.70.51719631.369100
2.48-2.535.80.46919571.49899.9
2.53-2.65.80.38919481.39799.9
2.6-2.675.80.31519461.51699.9
2.67-2.755.80.27219691.541100
2.75-2.835.90.22119561.533100
2.83-2.945.90.16919701.595100
2.94-3.055.90.13119771.614100
3.05-3.195.90.11419541.72100
3.19-3.365.90.08819661.853100
3.36-3.575.90.06919922.12100
3.57-3.855.80.06119812.513100
3.85-4.235.80.0519922.59699.9
4.23-4.855.80.04320102.519100
4.85-6.15.70.0420382.235100
6.1-505.30.03420992.14498.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mq4

3mq4


Resolution: 2.26→32.84 Å / Cor.coef. Fo:Fc: 0.9221 / Cor.coef. Fo:Fc free: 0.9076 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1984 5.04 %RANDOM
Rwork0.2011 ---
all0.2024 39402 --
obs0.2024 39363 --
Displacement parametersBiso max: 155.06 Å2 / Biso mean: 60.7113 Å2 / Biso min: 29.38 Å2
Baniso -1Baniso -2Baniso -3
1-10.7184 Å20 Å20 Å2
2--13.0832 Å20 Å2
3----23.8015 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.26→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 53 102 3530
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1195SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes536HARMONIC5
X-RAY DIFFRACTIONt_it3560HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion461SEMIHARMONIC5
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_contact3942SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3589HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4885HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion17.83
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2849 144 5.46 %
Rwork0.2366 2493 -
all0.2392 2637 -

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