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- PDB-3mq4: Metabotropic glutamate receptor mGluR7 complexed with LY341495 an... -

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Basic information

Entry
Database: PDB / ID: 3mq4
TitleMetabotropic glutamate receptor mGluR7 complexed with LY341495 antagonist
ComponentsMetabotropic glutamate receptor 7
KeywordsSIGNALING PROTEIN / GLUTAMATE RECEPTORS / MGLUR7 / DIMERIZATION / GLUTAMIC ACID BINDING / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / negative regulation of glutamate secretion / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / glutamate binding ...group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / glycosylation / negative regulation of glutamate secretion / serine binding / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / glutamate binding / axon development / presynaptic active zone / asymmetric synapse / regulation of synaptic transmission, glutamatergic / dendritic shaft / PDZ domain binding / sensory perception of sound / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell cortex / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / receptor complex / protein dimerization activity / axon / dendrite / calcium ion binding / membrane / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 7 / 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 7 / 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-Z99 / Metabotropic glutamate receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / He, H. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Cossar, D. / Bochkarev, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: mGluR7 complexed with LY341495
Authors: Dobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / He, H. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Cossar, D. / Bochkarev, A.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9913
Polymers53,6131
Non-polymers3782
Water00
1
A: Metabotropic glutamate receptor 7
hetero molecules

A: Metabotropic glutamate receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9826
Polymers107,2262
Non-polymers7554
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area1500 Å2
ΔGint-16 kcal/mol
Surface area36740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.673, 131.159, 140.644
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsdimer

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Components

#1: Protein Metabotropic glutamate receptor 7 / mGluR7


Mass: 53613.152 Da / Num. of mol.: 1 / Fragment: Ligand binding domain, residues 37-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPRC1G, GRM7, MGLUR7 / Plasmid: pFHMSP-LIC-C / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14831
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#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


Mass: 353.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19NO5 / Comment: antidepressant, antagonist*YM
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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 20.0% PEG 3350, 0.2M NaH2PO4. protein at 5mg/mL plus 2mM LY341495, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2010
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→26.87 Å / Num. obs: 12809 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 98.52 Å2 / Rsym value: 0.06 / Net I/σ(I): 46.29
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.12 / Rsym value: 0.78 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
BUSTER2.8.0refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS9

3ks9


Resolution: 2.8→27.6 Å / Cor.coef. Fo:Fc: 0.9082 / Cor.coef. Fo:Fc free: 0.8821 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined with BUSTER-TNT using TLS. The TLS records were excluded from the REMARK 3, since BUSTER-TNT TLS records contain characters not supported by PDB format
RfactorNum. reflection% reflectionSelection details
Rfree0.2933 626 4.9 %RANDOM
Rwork0.262 ---
obs0.2635 12769 --
Displacement parametersBiso mean: 114.18 Å2
Baniso -1Baniso -2Baniso -3
1--16.7052 Å20 Å20 Å2
2---3.908 Å20 Å2
3---20.6132 Å2
Refine analyzeLuzzati coordinate error obs: 0.666 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 27 0 2705
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092754HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.153759HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d811SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes421HARMONIC5
X-RAY DIFFRACTIONt_it2754HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.89
X-RAY DIFFRACTIONt_other_torsion19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3895
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_contact29534
LS refinement shellResolution: 2.8→3.07 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3224 161 5.35 %
Rwork0.2781 2846 -
all0.2806 3007 -

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