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- PDB-9hc0: Dark structure of the human metabotropic glutamate receptor 5 tra... -

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Basic information

Entry
Database: PDB / ID: 9hc0
TitleDark structure of the human metabotropic glutamate receptor 5 transmembrane domain bound to photoswitchable ligand alloswitch-1
ComponentsMetabotropic glutamate receptor 5,Endolysin
KeywordsSIGNALING PROTEIN / G protein-coupled receptor
Function / homology
Function and homology information


A2A adenosine receptor binding / sensory perception of hot stimulus / : / negative regulation of dendritic spine morphogenesis / 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 / operant conditioning / protein localization to nuclear inner membrane / positive regulation of cellular response to hypoxia ...A2A adenosine receptor binding / sensory perception of hot stimulus / : / negative regulation of dendritic spine morphogenesis / 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 / operant conditioning / protein localization to nuclear inner membrane / positive regulation of cellular response to hypoxia / positive regulation of long-term neuronal synaptic plasticity / positive regulation of sensory perception of pain / negative regulation of excitatory postsynaptic potential / positive regulation of dopamine secretion / desensitization of G protein-coupled receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / positive regulation of neural precursor cell proliferation / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / nuclear inner membrane / Neurexins and neuroligins / astrocyte projection / response to corticosterone / response to morphine / temperature homeostasis / protein tyrosine kinase activator activity / conditioned place preference / viral release from host cell by cytolysis / regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / regulation of long-term synaptic depression / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / dendritic shaft / response to amphetamine / 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 / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / dendritic spine / chemical synaptic transmission / host cell cytoplasm / response to ethanol / learning or memory / positive regulation of MAPK cascade / defense response to bacterium / response to antibiotic / neuronal cell body / regulation of DNA-templated transcription / dendrite / 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 / 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
Chem-4YI / 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: 2.33 Å
AuthorsKondo, Y. / Hatton, C. / Cheng, R. / Trabuco, M. / Glover, H. / Bertrand, Q. / Stierli, F. / Seidel, H.P. / Mason, T. / Sarma, S. ...Kondo, Y. / Hatton, C. / Cheng, R. / Trabuco, M. / Glover, H. / Bertrand, Q. / Stierli, F. / Seidel, H.P. / Mason, T. / Sarma, S. / Tellkamp, F. / Kepa, M. / Dworkowski, F. / Mehrabi, P. / Hennig, M. / Standfuss, J.
Funding supportEuropean Union, Switzerland, Germany, 4items
OrganizationGrant numberCountry
Innosuisse42711.1 IP-LSEuropean Union
Swiss National Science FoundationCRSII5_213507 Switzerland
Swiss National Science Foundation310030_207462 Switzerland
German Research Foundation (DFG)451079909 Germany
CitationJournal: Protein Sci. / Year: 2025
Title: Apo-state structure of the metabotropic glutamate receptor 5 transmembrane domain obtained using a photoswitchable ligand.
Authors: Kondo, Y. / Hatton, C. / Cheng, R. / Trabuco, M. / Glover, H. / Bertrand, Q. / Stierli, F. / Seidel, H.P. / Mason, T. / Sarma, S. / Tellkamp, F. / Kepa, M. / Dworkowski, F. / Mehrabi, P. / ...Authors: Kondo, Y. / Hatton, C. / Cheng, R. / Trabuco, M. / Glover, H. / Bertrand, Q. / Stierli, F. / Seidel, H.P. / Mason, T. / Sarma, S. / Tellkamp, F. / Kepa, M. / Dworkowski, F. / Mehrabi, P. / Hennig, M. / Standfuss, J.
History
DepositionNov 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,6967
Polymers49,9171
Non-polymers1,7796
Water39622
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.221, 43.363, 82.642
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 49916.641 Da / Num. of mol.: 1 / Mutation: E579A,N667Y,I669A,G675M,T742A,S753A
Source method: isolated from a genetically manipulated source
Details: metabotropic glutamate receptor 5 with T4 lysozyme insertion and thermostabilising mutations E579A, N667Y, I669A, G675M, T742A, S753A
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: GRM5, GPRC1E, MGLUR5, E / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P41594, UniProt: P00720, lysozyme
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-4YI / 2-chloranyl-~{N}-[2-methoxy-4-[(~{E})-pyridin-2-yldiazenyl]phenyl]benzamide


Mass: 366.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.2
Details: PEG300, di-ammonium hydrogen phosphate, 1,6-hexanediol, BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→49.31 Å / Num. obs: 14590 / % possible obs: 67.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 49.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.8
Reflection shellResolution: 2.33→2.58 Å / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 128 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→49.31 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.1061
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 1460 10.01 %
Rwork0.229 13130 -
obs0.2332 14590 67.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.88 Å2
Refinement stepCycle: LAST / Resolution: 2.33→49.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 126 22 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333443
X-RAY DIFFRACTIONf_angle_d0.59484639
X-RAY DIFFRACTIONf_chiral_restr0.0406531
X-RAY DIFFRACTIONf_plane_restr0.006578
X-RAY DIFFRACTIONf_dihedral_angle_d13.1031309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.410.3108120.2967116X-RAY DIFFRACTION5.91
2.41-2.510.3813300.3013258X-RAY DIFFRACTION13.72
2.51-2.630.3579570.3026514X-RAY DIFFRACTION26.53
2.63-2.760.3169930.3077841X-RAY DIFFRACTION42.88
2.76-2.940.33571820.30431629X-RAY DIFFRACTION84.23
2.94-3.160.31752120.30281922X-RAY DIFFRACTION99.53
3.16-3.480.29432170.24251939X-RAY DIFFRACTION99.13
3.48-3.990.28742150.22181944X-RAY DIFFRACTION98.32
3.99-5.020.23192150.2021939X-RAY DIFFRACTION98.4
5.02-49.310.24662270.20032028X-RAY DIFFRACTION99.03

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