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- PDB-4or2: Human class C G protein-coupled metabotropic glutamate receptor 1... -

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Basic information

Entry
Database: PDB / ID: 4or2
TitleHuman class C G protein-coupled metabotropic glutamate receptor 1 in complex with a negative allosteric modulator
ComponentsSoluble cytochrome b562, Metabotropic glutamate receptor 1
KeywordsSIGNALING PROTEIN / Human metabotropic glutamate receptor 1 / allosteric modulator / novel protein engineering / GPCR network / membrane protein / PSI-Biology / Structural Genomics / GPCR / membrane
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor dimeric complex / G protein-coupled receptor homodimeric complex / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / cellular response to electrical stimulus / regulation of sensory perception of pain / G protein-coupled glutamate receptor signaling pathway / L-glutamate import across plasma membrane / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / sensory perception of pain / regulation of synaptic transmission, glutamatergic / locomotory behavior / G protein-coupled receptor activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / Sensory perception of sweet, bitter, and umami (glutamate) taste / chemical synaptic transmission / G alpha (q) signalling events / positive regulation of MAPK cascade / electron transfer activity / periplasmic space / iron ion binding / G protein-coupled receptor signaling pathway / dendrite / glutamatergic synapse / heme binding / nucleus / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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, metabotropic glutamate receptor 1 / Metabotropic glutamate receptor, Homer-binding domain / Homer-binding domain of metabotropic glutamate receptor / GluR_Homer-bdg / 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. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
CHOLESTEROL / Chem-FM9 / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Soluble cytochrome b562 / Metabotropic glutamate receptor 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWu, H. / Wang, C. / Gregory, K.J. / Han, G.W. / Cho, H.P. / Xia, Y. / Niswender, C.M. / Katritch, V. / Cherezov, V. / Conn, P.J. ...Wu, H. / Wang, C. / Gregory, K.J. / Han, G.W. / Cho, H.P. / Xia, Y. / Niswender, C.M. / Katritch, V. / Cherezov, V. / Conn, P.J. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2014
Title: Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator
Authors: Wu, H. / Wang, C. / Gregory, K.J. / Han, G.W. / Cho, H.P. / Xia, Y. / Niswender, C.M. / Katritch, V. / Meiler, J. / Cherezov, V. / Conn, P.J. / Stevens, R.C.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Apr 1, 2015Group: Database references
Revision 1.4Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562, Metabotropic glutamate receptor 1
B: Soluble cytochrome b562, Metabotropic glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,11516
Polymers86,5102
Non-polymers4,60514
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11 kcal/mol
Surface area35110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.361, 86.552, 168.277
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Soluble cytochrome b562, Metabotropic glutamate receptor 1 / Cytochrome b-562 / mGluR1


Mass: 43254.863 Da / Num. of mol.: 2 / Mutation: M7W, H102I, R106L
Source method: isolated from a genetically manipulated source
Details: Chimera protein of Soluble cytochrome b562 from Escherichia coli (P0ABE7) and residues 581-860 from Metabotropic glutamate receptor 1 from Homo sapiens (Q13255).
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, GRM1_HUMAN, GPRC1A, GRM1, MGLUR1 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P0ABE7, UniProt: Q13255

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Non-polymers , 6 types, 27 molecules

#2: Chemical ChemComp-FM9 / 4-fluoro-N-methyl-N-{4-[6-(propan-2-ylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl}benzamide


Mass: 371.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18FN5OS
#3: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7
Details: 100mM HEPES (pH 7.0), 27-30% (v/v) PEG 400, 80-120mM (NH4)2HPO4, 4-8mM TCEP, Lipidic Cubic Phase (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 24533 / % possible obs: 98.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 84.6 Å2 / Rmerge(I) obs: 0.132 / Net I/σ(I): 13.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
AutoSolphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: Experimental Phasing by using Ta6Br12 soak

Resolution: 2.8→35.68 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.9145 / SU R Cruickshank DPI: 1.673 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1247 5.09 %RANDOM
Rwork0.227 ---
obs0.2291 24480 98.18 %-
Displacement parametersBiso mean: 98.21 Å2
Baniso -1Baniso -2Baniso -3
1-9.8067 Å20 Å20 Å2
2--8.28 Å20 Å2
3----18.0867 Å2
Refine analyzeLuzzati coordinate error obs: 0.534 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 290 13 5895
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016028HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.118240HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2823SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes842HARMONIC5
X-RAY DIFFRACTIONt_it6028HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion3.08
X-RAY DIFFRACTIONt_chiral_improper_torsion874SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7369SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2934 115 4.22 %
Rwork0.2307 2612 -
all0.2333 2727 -
obs--98.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.2126-3.4382-5.82085.04113.83758.27690.20650.2496-0.2209-0.55480.3948-0.31040.05130.8269-0.6013-0.1240.02810.1524-0.1939-0.1246-0.093936.8045-6.67173.8346
20.9312-0.0889-0.07252.1613-0.41342.3002-0.131-0.1427-0.17980.2-0.0486-0.02580.2080.35540.1796-0.24450.04250.0135-0.09630.0914-0.112521.1346-19.919442.0795
38.4895-3.21595.56755.8059-5.82087.36490.0480.72790.0387-0.58120.04070.4457-0.2244-0.2975-0.08870.08490.1824-0.1722-0.0953-0.0319-0.2673-0.5716.90462.5525
41.2088-0.21-0.15042.06490.26392.1657-0.0502-0.1570.13050.0993-0.0176-0.236-0.1650.26390.0678-0.2175-0.03190.0171-0.1444-0.026-0.104510.551316.294243.832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1002 - A|1106 }A2 - 106
2X-RAY DIFFRACTION2{ A|581 - A|843 }A581 - 843
3X-RAY DIFFRACTION3{ B|1002 - B|1106 }B2 - 106
4X-RAY DIFFRACTION4{ B|581 - B|846 }B581 - 846

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