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- PDB-6ffi: Crystal Structure of mGluR5 in complex with MMPEP at 2.2 A -

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Basic information

Entry
Database: PDB / ID: 6ffi
TitleCrystal Structure of mGluR5 in complex with MMPEP at 2.2 A
ComponentsMetabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
KeywordsMEMBRANE PROTEIN / 7TM / RECEPTOR / GPCR / MEMBRANE-PROTEIN / SIGNALING PROTEIN
Function / homology
Function and homology information


A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) ...A2A adenosine receptor binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / phospholipase C-activating G protein-coupled glutamate receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / astrocyte projection / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / protein tyrosine kinase activator activity / viral release from host cell by cytolysis / regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / positive regulation of calcium-mediated signaling / dendritic shaft / protein tyrosine kinase binding / learning / locomotory behavior / synapse organization / postsynaptic density membrane / G protein-coupled receptor activity / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / chemical synaptic transmission / G alpha (q) signalling events / dendritic spine / host cell cytoplasm / learning or memory / positive regulation of MAPK cascade / defense response to bacterium / neuronal cell body / dendrite / regulation of DNA-templated transcription / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 5 / 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 ...GPCR, family 3, metabotropic glutamate receptor 5 / 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 / 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 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Lysozyme-like domain superfamily
Similarity search - Domain/homology
2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine / OLEIC ACID / Endolysin / Metabotropic glutamate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsChristopher, J.A. / Orgovan, Z. / Congreve, M. / Dore, A.S. / Errey, J.C. / Marshall, F.H. / Mason, J.S. / Okrasa, K. / Rucktooa, P. / Serrano-Vega, M.J. ...Christopher, J.A. / Orgovan, Z. / Congreve, M. / Dore, A.S. / Errey, J.C. / Marshall, F.H. / Mason, J.S. / Okrasa, K. / Rucktooa, P. / Serrano-Vega, M.J. / Ferenczy, G.G. / Keseru, G.M.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu5) X-ray Structures.
Authors: Christopher, J.A. / Orgovan, Z. / Congreve, M. / Dore, A.S. / Errey, J.C. / Marshall, F.H. / Mason, J.S. / Okrasa, K. / Rucktooa, P. / Serrano-Vega, M.J. / Ferenczy, G.G. / Keseru, G.M.
History
DepositionJan 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Apr 24, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,25510
Polymers49,8601
Non-polymers2,3969
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein elutes as a monomer on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint25 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.822, 43.424, 81.976
Angle α, β, γ (deg.)90.000, 98.930, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Metabotropic glutamate receptor 5,Endolysin,Metabotropic glutamate receptor 5 / mGluR5 / Lysis protein / Lysozyme / Muramidase / mGluR5


Mass: 49859.586 Da / Num. of mol.: 1
Fragment: MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5,MGLUR5
Mutation: E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A ...Mutation: E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A,E579A N667Y I669A G675M T742A S753A
Source method: isolated from a genetically manipulated source
Details: Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 ...Details: Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.,Chimeric construct of Human mGLU5 (GRM5) with a Bacteriophage T4 Lysozyme (P00720) insertion in intracellular loop 2 between residues LYS678 and LYS679.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GRM5, GPRC1E, MGLUR5 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P41594, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Fragment: T4L / Mutation: C54T C97A
Source method: isolated from a genetically manipulated source
Formula: C18H34O2 / Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: lysozyme
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-D8B / 2-[2-(3-methoxyphenyl)ethynyl]-6-methyl-pyridine


Mass: 223.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.52 Å3/Da / Density % sol: 51.16 % / Mosaicity: 0.14 °
Crystal growTemperature: 293.1 K / Method: lipidic cubic phase / pH: 6.8
Details: 24-34% V/V PEG400, 0.2 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M MES, PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.2→30.81 Å / Num. obs: 24147 / % possible obs: 94.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 33.161 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.098 / Rrim(I) all: 0.174 / Net I/σ(I): 7.2 / Num. measured all: 60498 / Scaling rejects: 142
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.272.61.03821510.4290.7221.27397.5
9.07-30.812.70.0453310.9950.0290.05483.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.2.17data scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OO9

4oo9


Resolution: 2.2→19.991 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.35
RfactorNum. reflection% reflection
Rfree0.2693 1164 4.86 %
Rwork0.2264 --
obs0.2284 23969 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.8 Å2 / Biso mean: 28.89 Å2 / Biso min: 6.6 Å2
Refinement stepCycle: final / Resolution: 2.2→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 127 142 3486
Biso mean--40.98 32.4 -
Num. residues----410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043411
X-RAY DIFFRACTIONf_angle_d0.8274592
X-RAY DIFFRACTIONf_chiral_restr0.055527
X-RAY DIFFRACTIONf_plane_restr0.004557
X-RAY DIFFRACTIONf_dihedral_angle_d14.3981290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30.40871540.32732862301696
2.3-2.42110.34771580.29792866302495
2.4211-2.57250.33261600.28882917307797
2.5725-2.77060.40211230.26332865298895
2.7706-3.04860.28021300.23452819294993
3.0486-3.48770.28731490.21682849299894
3.4877-4.38650.20171440.1862845298992
4.3865-19.99170.22381460.19882782292889

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