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- PDB-9n8y: Cryo EM Structure of Full Length mGluR8 Bound to Agonist L-AP4 an... -

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Basic information

Entry
Database: PDB / ID: 9n8y
TitleCryo EM Structure of Full Length mGluR8 Bound to Agonist L-AP4 and PAM VU6005649
ComponentsMetabotropic glutamate receptor 8
KeywordsMEMBRANE PROTEIN / GPCR / metabotropic glutamate receptor / synaptic protein / signaling protein
Function / homology
Function and homology information


group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / regulation of synaptic transmission, glutamatergic / visual perception / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G alpha (i) signalling events / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 8 / 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, metabotropic glutamate receptor 8 / 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 / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
: / (2S)-2-amino-4-phosphonobutanoic acid / Metabotropic glutamate receptor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsMarx, D.C. / Levitz, J.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM148001 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS129904 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS129320 United States
CitationJournal: To Be Published
Title: Structural Diversity of Metabotropic Glutamate Receptor/Beta-Arrestin Coupling
Authors: Marx, D.C. / Gonzalex-Hernandez, A.J. / Huynh, K. / Strauss, A. / Rico, C. / Siepe, D. / Gallo, P.N. / Lee, J. / Sharghi, S. / Arefin, A. / Broichhagen, J. / Eliezer, D. / Kalocsay, M. / ...Authors: Marx, D.C. / Gonzalex-Hernandez, A.J. / Huynh, K. / Strauss, A. / Rico, C. / Siepe, D. / Gallo, P.N. / Lee, J. / Sharghi, S. / Arefin, A. / Broichhagen, J. / Eliezer, D. / Kalocsay, M. / Khelashvilli, G. / Levitz, J.
History
DepositionFeb 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 8
B: Metabotropic glutamate receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,9876
Polymers187,9072
Non-polymers1,0814
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Metabotropic glutamate receptor 8 / mGluR8


Mass: 93953.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM8, GPRC1H, MGLUR8 / Cell line (production host): HEK GNTI- / Production host: Homo sapiens (human) / References: UniProt: O00222
#2: Chemical ChemComp-E7P / (2S)-2-amino-4-phosphonobutanoic acid


Mass: 183.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: agonist*YM
#3: Chemical ChemComp-A1BWG / (3P,8S)-3-(2,3-difluoro-4-methoxyphenyl)-2,5-dimethyl-7-(trifluoromethyl)pyrazolo[1,5-a]pyrimidine


Mass: 357.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12F5N3O
Has ligand of interestN
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: Metabotropic Glutamate Receptor 8 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.26 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338052 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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