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- PDB-5c5c: Human metabotropic glutamate receptor 7, extracellular ligand bin... -

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Basic information

Entry
Database: PDB / ID: 5c5c
TitleHuman metabotropic glutamate receptor 7, extracellular ligand binding domain
ComponentsMetabotropic glutamate receptor 7
KeywordsSIGNALING PROTEIN / GLUTAMATE RECEPTORS / GLUTAMIC ACID BINDING / MGLUR7 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / glycosylation / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / 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 / glycosylation / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / adenylate cyclase inhibitor activity / 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 / presynaptic active zone / axon development / asymmetric synapse / regulation of synaptic transmission, glutamatergic / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / PDZ domain binding / sensory perception of sound / cell cortex / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / protein dimerization activity / receptor complex / 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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...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 / 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
Metabotropic glutamate receptor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.862 Å
AuthorsDong, A. / Dobrovetsky, E. / Hutchinson, A. / Tempel, W. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Human metabotropic glutamate receptor 7, extracellular ligand binding domain
Authors: Dobrovetsky, E. / Dong, A. / Hutchinson, A. / Tempel, W. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / citation_author / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _audit_author.pdbx_ordinal / _chem_comp.name ..._audit_author.pdbx_ordinal / _chem_comp.name / _chem_comp.type / _citation_author.ordinal / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,00716
Polymers53,6131
Non-polymers39315
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-21 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.175, 101.203, 55.318
Angle α, β, γ (deg.)90.000, 110.460, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Metabotropic glutamate receptor 7 / / mGluR7


Mass: 53613.152 Da / Num. of mol.: 1 / Mutation: C249S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM7, GPRC1G, MGLUR7 / Plasmid: pFHMSP-LIC-N / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q14831
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M K2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 44656 / % possible obs: 97.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Χ2: 1.011 / Net I/av σ(I): 36.25 / Net I/σ(I): 10.1 / Num. measured all: 297932
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.8960.78120850.8420.3350.8520.71891.4
1.89-1.936.20.59521500.9030.2520.6470.72294.5
1.93-1.966.40.50421890.9350.2110.5470.74895.8
1.96-26.60.4621790.9450.1910.4980.73896.9
2-2.056.80.34822740.9650.1440.3770.7697.6
2.05-2.096.80.29422030.9790.1210.3180.79497.4
2.09-2.156.80.23622160.9850.0970.2550.8197.7
2.15-2.216.90.19122350.9890.0790.2070.81897.6
2.21-2.276.90.16922190.9910.070.1830.84498.1
2.27-2.346.80.14322430.9940.0590.1550.84298
2.34-2.436.80.12422570.9940.0510.1340.85998.1
2.43-2.526.80.10122550.9960.0420.1090.90598.3
2.52-2.646.80.08122350.9980.0340.0880.91498.5
2.64-2.786.80.0722510.9980.0290.075198.7
2.78-2.956.80.05722550.9980.0240.0621.14998.6
2.95-3.186.80.04922740.9990.020.0531.37299
3.18-3.56.70.04422690.9990.0180.0471.64899.1
3.5-4.016.60.03622780.9990.0150.0391.65799.3
4.01-5.056.50.0323020.9990.0130.0321.38699.5
5.05-506.60.03122870.9980.0140.0341.44597.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.06 Å31.91 Å
Translation2.06 Å31.91 Å

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.5.7phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MQ4

3mq4


Resolution: 1.862→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2512 / WRfactor Rwork: 0.204 / FOM work R set: 0.801 / SU B: 3.605 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1334 / SU Rfree: 0.1328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1420 3.2 %RANDOM
Rwork0.2061 ---
obs0.2075 43231 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.16 Å2 / Biso mean: 43.798 Å2 / Biso min: 25.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å22.57 Å2
2---3.87 Å20 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 1.862→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 33 83 3352
Biso mean--50.58 45.39 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193426
X-RAY DIFFRACTIONr_bond_other_d0.0010.023095
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9424681
X-RAY DIFFRACTIONr_angle_other_deg0.90937067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6145451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06924.581155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6915499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3651518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
X-RAY DIFFRACTIONr_mcbond_it2.2414.4951780
X-RAY DIFFRACTIONr_mcbond_other2.2394.4931779
X-RAY DIFFRACTIONr_mcangle_it3.5976.7172233
LS refinement shellResolution: 1.862→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 97 -
Rwork0.283 2945 -
all-3042 -
obs--90.37 %

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