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- PDB-8x0h: Human FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqua... -

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Basic information

Entry
Database: PDB / ID: 8x0h
TitleHuman FL Metabotropic glutamate receptor 5, mGlu5-5M with quisqualate, Rcc conformation
ComponentsMetabotropic glutamate receptor 5
KeywordsMEMBRANE PROTEIN / G-PROTEIN COUPLED RECEPTORS / SIGNAL TRANSDUCTION / METABOTROPIC GLUTAMATE RECEPTOR / Agonist / active state
Function / homology
Function and homology information


A2A adenosine receptor binding / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / 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 ...A2A adenosine receptor binding / G protein-coupled receptor activity involved in regulation of postsynaptic membrane potential / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / 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 / regulation of synaptic transmission, glutamatergic / positive regulation of calcium-mediated signaling / dendritic shaft / protein tyrosine kinase binding / learning / locomotory behavior / synapse organization / G protein-coupled receptor activity / postsynaptic density membrane / Schaffer collateral - CA1 synapse / cognition / cellular response to amyloid-beta / chemical synaptic transmission / G alpha (q) signalling events / dendritic spine / positive regulation of MAPK cascade / learning or memory / 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 / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Chem-QUS / Metabotropic glutamate receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsVinothkumar, K.R. / Lebon, G. / Cannone, G.
Funding support India, France, 3items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR12422/MED/31/287/204 India
Other governmentRTI4006 India
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0019 France
CitationJournal: Nat Commun / Year: 2025
Title: Conformational diversity in class C GPCR positive allosteric modulation.
Authors: Giuseppe Cannone / Ludovic Berto / Fanny Malhaire / Gavin Ferguson / Aurelien Fouillen / Stéphanie Balor / Joan Font-Ingles / Amadeu Llebaria / Cyril Goudet / Abhay Kotecha / Vinothkumar K ...Authors: Giuseppe Cannone / Ludovic Berto / Fanny Malhaire / Gavin Ferguson / Aurelien Fouillen / Stéphanie Balor / Joan Font-Ingles / Amadeu Llebaria / Cyril Goudet / Abhay Kotecha / Vinothkumar K R / Guillaume Lebon /
Abstract: The metabotropic glutamate receptors (mGlus) are class C G protein-coupled receptors (GPCR) that form obligate dimers activated by the major excitatory neurotransmitter L-glutamate. The architecture ...The metabotropic glutamate receptors (mGlus) are class C G protein-coupled receptors (GPCR) that form obligate dimers activated by the major excitatory neurotransmitter L-glutamate. The architecture of mGlu receptor comprises an extracellular Venus-Fly Trap domain (VFT) connected to the transmembrane domain (7TM) through a Cysteine-Rich Domain (CRD). The binding of L-glutamate in the VFTs and subsequent conformational change results in the signal being transmitted to the 7TM inducing G protein binding and activation. The mGlu receptors signal transduction can be allosterically potentiated by positive allosteric modulators (PAMs) binding to the 7TMs, which are of therapeutic interest in various neurological disorders. Here, we report the cryoEM structures of metabotropic glutamate receptor 5 (mGlu) purified with three chemically and pharmacologically distinct PAMs. We find that the PAMs modulate the receptor equilibrium through their different binding modes, revealing how their interactions in the 7TMs impact the mGlu receptor conformational landscape and function. In addition, we identified a PAM-free but agonist-bound intermediate state that also reveals interactions mediated by intracellular loop 2. The activation of mGlu receptor is a multi-step process in which the binding of the PAMs in the 7TM modulates the equilibrium towards the active state.
History
DepositionNov 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Jan 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 5
B: Metabotropic glutamate receptor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,2046
Polymers187,3832
Non-polymers8214
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Metabotropic glutamate receptor 5


Mass: 93691.492 Da / Num. of mol.: 2 / Mutation: T742A, S753A, T777A, I799A, A813L,N445A,H350L
Source method: isolated from a genetically manipulated source
Details: The construct has tags and protease cleavage site at its N-term (DYKDDDDKHHHHHHHHHHLEVLFQGP) and when compared to uniprot it starts at 21 and ends at 856. For CryoEM, the tag is cleaved and ...Details: The construct has tags and protease cleavage site at its N-term (DYKDDDDKHHHHHHHHHHLEVLFQGP) and when compared to uniprot it starts at 21 and ends at 856. For CryoEM, the tag is cleaved and the protein used for experiment starts at QSSE but residues starting RR have been modeled. There are 5 thermostabilising mutations (T742A, S753A, T777A, I799A, A813L). Residue N445 is mutated to remove glycosylation. An additional mutation H350L is engineered for a nanobody to bind. Each monomer has one sugar modeled and 10 disulfide bonds.
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM5 / Plasmid: BacMaM / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: P41594
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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
#3: Chemical ChemComp-QUS / (S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID / QUISQUALATE


Mass: 189.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7N3O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mGlu Receptor bound to quisqualate, in Rcc conformation
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI- / Plasmid: BacMaM
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
125 mMHEPES1
2150 mMSodium Chloride1
30.03 %dodecyl maltoside1
40.006 %cholesterol hemisuccinate1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Data was collected in EFTEM mode with Bioquantum K3
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 59523 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.9 sec. / Electron dose: 49.55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18710
Details: Electron flux was 18.4 e/p/s and total number of frames were 50.
Image scansSampling size: 5 µm / Width: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF Chimera1.15model fitting
8Coot0.9.8.7model fitting
13cryoSPARC3D reconstruction
14PHENIX1.20.1-4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3416003
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 344232 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingB value: 88.3 / Protocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain residue rangeInitial refinement model-IDPdb chain residue rangeSource nameDetails
17FD9

7fd9

A7FD9565-8271565-827PDB
2D_130004238125-5102OtherActive conformation from same data
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412599
ELECTRON MICROSCOPYf_angle_d0.64417065
ELECTRON MICROSCOPYf_dihedral_angle_d6.0871724
ELECTRON MICROSCOPYf_chiral_restr0.0451915
ELECTRON MICROSCOPYf_plane_restr0.0042145

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