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- PDB-9uyq: Cryo-EM structure of a class C GPCR (Class 2) -

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Basic information

Entry
Database: PDB / ID: 9uyq
TitleCryo-EM structure of a class C GPCR (Class 2)
ComponentsMetabotropic glutamate receptor 6
KeywordsMEMBRANE PROTEIN / GPCR
Function / homology
Function and homology information


new growing cell tip / positive regulation of calcium ion import across plasma membrane / detection of light stimulus involved in visual perception / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / detection of visible light / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / regulation of synaptic transmission, glutamatergic / locomotory behavior ...new growing cell tip / positive regulation of calcium ion import across plasma membrane / detection of light stimulus involved in visual perception / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / detection of visible light / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / regulation of synaptic transmission, glutamatergic / locomotory behavior / G protein-coupled receptor activity / chemical synaptic transmission / G alpha (i) signalling events / Golgi membrane / dendrite / endoplasmic reticulum membrane / synapse / protein homodimerization activity / plasma membrane
Similarity search - Function
GPCR, family 3, metabotropic glutamate receptor 6 / 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 6 / 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
PHOSPHOSERINE / Metabotropic glutamate receptor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsLee, S.Y. / Yun, Y. / Ji, J.S. / Jeong, H. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology Foundation Korea, Republic Of
CitationJournal: Nat Commun / Year: 2026
Title: CryoEM structure of mGlu6 captures receptor activation prior to G protein coupling.
Authors: Seo Young Lee / Chu-Ting Chang / Yaejin Yun / Jeong Seok Ji / Kirill A Martemyanov / Hyung Ho Lee /
Abstract: The metabotropic glutamate receptor 6 (mGlu6) is essential for synaptic communication of rod photoreceptors, and mutations in mGlu6 lead to a blinding disorder. However, its structural organization ...The metabotropic glutamate receptor 6 (mGlu6) is essential for synaptic communication of rod photoreceptors, and mutations in mGlu6 lead to a blinding disorder. However, its structural organization remains unknown. Here, we present the structure of agonist-bound mGlu6, revealing an asymmetric dimer arrangement in the absence of a G protein. This indicates that agonist binding alone can induce the homodimeric receptor asymmetry in metabotropic glutamate receptors and structurally prime mGlu6 for activation by pre-organizing the transmembrane domain dimer interface for G protein binding. The structure also identifies noncanonical interactions between the cysteine-rich domain and extracellular loop 2, forming a unique interface that likely stabilizes the activation state. Mutational analyses of this interface reveal its role in maintaining rapid Gαo activation and surface targeting. The structure also permits mechanistic investigation of congenital stationary night blindness and reveals diverse effects of pathogenic mutations on surface trafficking, Gαo coupling, and activation dynamics, including unexpected gain-of-function. These results provide critical insight into the intermediate asymmetric structure of mGlu6 and offer a molecular framework for understanding the pathogenesis of inherited retinal disorders.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Metabotropic glutamate receptor 6
A: Metabotropic glutamate receptor 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,4494
Polymers191,0792
Non-polymers3702
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 6 / mGluR6


Mass: 95539.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRM6, GPRC1F, MGLUR6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15303
#2: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8NO6P / Feature type: SUBJECT OF INVESTIGATION
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: Cryo-EM structure of a class C GPCR (Global, without symmetry)
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 67.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146427 / Symmetry type: POINT
RefinementHighest resolution: 3.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312220
ELECTRON MICROSCOPYf_angle_d0.49216623
ELECTRON MICROSCOPYf_dihedral_angle_d3.621704
ELECTRON MICROSCOPYf_chiral_restr0.0371896
ELECTRON MICROSCOPYf_plane_restr0.0052133

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