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- PDB-4oo9: Structure of the human class C GPCR metabotropic glutamate recept... -

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Basic information

Entry
Database: PDB / ID: 4oo9
TitleStructure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator mavoglurant
ComponentsMetabotropic glutamate receptor 5, Lysozyme, Metabotropic glutamate receptor 5 chimera
KeywordsMEMBRANE PROTEIN / 7TM / receptor / G-protein / cysteine-S-acetamide
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 / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity ...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 / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / Neurexins and neuroligins / astrocyte projection / protein tyrosine kinase activator activity / regulation of synaptic transmission, glutamatergic / viral release from host cell by cytolysis / peptidoglycan catabolic process / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / dendritic shaft / learning / locomotory behavior / G protein-coupled receptor activity / synapse organization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / G alpha (q) signalling events / chemical synaptic transmission / 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 3. / G-protein coupled receptors family 3 signature 2. / GPCR, family 3, nine cysteines domain ...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 3. / 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 / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Lysozyme - #40 / 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 / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Mavoglurant / OLEIC ACID / Endolysin / Metabotropic glutamate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. ...Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. / Weir, M. / Wiggin, G.R. / Marshall, F.H.
CitationJournal: Nature / Year: 2014
Title: Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain.
Authors: Dore, A.S. / Okrasa, K. / Patel, J.C. / Serrano-Vega, M. / Bennett, K. / Cooke, R.M. / Errey, J.C. / Jazayeri, A. / Khan, S. / Tehan, B. / Weir, M. / Wiggin, G.R. / Marshall, F.H.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Atomic model / Non-polymer description ...Atomic model / Non-polymer description / Source and taxonomy / Structure summary
Revision 1.3Aug 6, 2014Group: Database references
Revision 1.4Jul 15, 2015Group: Source and taxonomy
Revision 1.5Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.6Sep 20, 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_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.pdbx_leaving_atom_flag / _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: Metabotropic glutamate receptor 5, Lysozyme, Metabotropic glutamate receptor 5 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5557
Polymers49,9171
Non-polymers1,6386
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.242, 43.555, 82.049
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-4143-

HOH

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Components

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


Mass: 49916.641 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GRM5, GPRC1E, MGLUR5, E / Plasmid: FastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P41594, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-2U8 / Mavoglurant / methyl (3aR,4S,7aR)-4-hydroxy-4-[(3-methylphenyl)ethynyl]octahydro-1H-indole-1-carboxylate


Mass: 313.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23NO3
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS A CHIMERA COMPRISING RESIDUES 569-678 AND 679-836 OF GLUR5 SEPARATED BY RESIDUES 2-162 OF LYSOZYME.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.37 %
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, LIPIDIC CUBIC PHASE, temperature 293.1K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.6→80.955 Å / Num. all: 14800 / Num. obs: 14800 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 7.4
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.8 / % possible all: 94.8

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3EML, 3UON, 4DAJ, 4DKL, 4DJH, 3V2Y, 4EA3, AND 1U19

3eml

3uon

4daj

4dkl

4djh

3v2y

4ea3

1u19


Resolution: 2.6→29.74 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 30.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 691 4.68 %
Rwork0.2392 --
obs0.2409 14779 94.06 %
all-14779 -
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 97 46 3355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033373
X-RAY DIFFRACTIONf_angle_d0.6584555
X-RAY DIFFRACTIONf_dihedral_angle_d11.5311280
X-RAY DIFFRACTIONf_chiral_restr0.043526
X-RAY DIFFRACTIONf_plane_restr0.003551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80060.37621310.30782801X-RAY DIFFRACTION95
2.8006-3.08220.26351400.2782855X-RAY DIFFRACTION96
3.0822-3.52760.32851310.26152851X-RAY DIFFRACTION95
3.5276-4.4420.2631410.22132813X-RAY DIFFRACTION94
4.442-29.74150.23741480.20932768X-RAY DIFFRACTION90
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)
10.30760.10140.26720.10180.04890.0372-0.10430.0604-0.2340.1240.01690.24860.18730.07250.02310.2019-0.065-0.0220.1974-0.00460.2147-33.6069-13.959441.117
2-0.25270.2064-0.1660.2104-0.06840.5866-0.1206-0.1167-0.01010.00210.0662-0.0498-0.1231-0.2951-0.12220.14290.06470.01110.3198-0.02990.1618-14.35474.21837.9223
30.5221-0.21320.14090.2787-0.10730.2468-0.0313-0.0197-0.01490.0105-0.0414-0.03310.0518-0.0183-0.04980.187-0.0287-0.00430.11950.01090.1967-22.7584-5.673538.5019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 568 through 640 )
2X-RAY DIFFRACTION2chain 'A' and (resid 641 through 689 ) or chain 'A' and (resid 1002 through 1162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 690 through 832 )

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