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- EMDB-63210: Cryo-EM structure of a class C GPCR (Global, without symmetry) -

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Basic information

Entry
Database: EMDB / ID: EMD-63210
TitleCryo-EM structure of a class C GPCR (Global, without symmetry)
Map data
Sample
  • Complex: Cryo-EM structure of a class C GPCR (Global, without symmetry)
    • Protein or peptide: Metabotropic glutamate receptor 6
  • Ligand: PHOSPHOSERINE
KeywordsGPCR / MEMBRANE PROTEIN
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
Metabotropic glutamate receptor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLee SY / Yun Y / Ji JS / Jeong H / Lee HH
Funding support Korea, Republic Of, 1 items
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
DepositionJan 18, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63210.png

Downloads & links

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Map

FileDownload / File: emd_63210.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 432 pix.
= 366.336 Å		0.85 Å/pix.
x 432 pix.
= 366.336 Å		0.85 Å/pix.
x 432 pix.
= 366.336 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.98913 - 3.20076
Average (Standard dev.)-0.0005406136 (±0.04256429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 366.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63210_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_63210_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of a class C GPCR (Global, without symmetry)

EntireName: Cryo-EM structure of a class C GPCR (Global, without symmetry)
Components
  • Complex: Cryo-EM structure of a class C GPCR (Global, without symmetry)
    • Protein or peptide: Metabotropic glutamate receptor 6
  • Ligand: PHOSPHOSERINE

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Supramolecule #1: Cryo-EM structure of a class C GPCR (Global, without symmetry)

SupramoleculeName: Cryo-EM structure of a class C GPCR (Global, without symmetry)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Metabotropic glutamate receptor 6

MacromoleculeName: Metabotropic glutamate receptor 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.539266 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GLARAAGSVR LAGGLTLGGL FPVHARGAAG RACGQLKKEQ GVHRLEAMLY ALDRVNADPE LLPGVRLGAR LLDTCSRDTY ALEQALSFV QALIRGRGDG DEVGVRCPGG VPPLRPAPPE RVVAVVGASA SSVSIMVANV LRLFAIPQIS YASTAPELSD S TRYDFFSR ...String:
GLARAAGSVR LAGGLTLGGL FPVHARGAAG RACGQLKKEQ GVHRLEAMLY ALDRVNADPE LLPGVRLGAR LLDTCSRDTY ALEQALSFV QALIRGRGDG DEVGVRCPGG VPPLRPAPPE RVVAVVGASA SSVSIMVANV LRLFAIPQIS YASTAPELSD S TRYDFFSR VVPPDSYQAQ AMVDIVRALG WNYVSTLASE GNYGESGVEA FVQISREAGG VCIAQSIKIP REPKPGEFSK VI RRLMETP NARGIIIFAN EDDIRRVLEA ARQANLTGHF LWVGSDSWGA KTSPILSLED VAVGAITILP KRASIDGFDQ YFM TRSLEN NRRNIWFAEF WEENFNCKLT SSGTQSDDST RKCTGEERIG RDSTYEQEGK VQFVIDAVYA IAHALHSMHQ ALCP GHTGL CPAMEPTDGR MLLQYIRAVR FNGSAGTPVM FNENGDAPGR YDIFQYQATN GSASSGGYQA VGQWAETLRL DVEAL QWSG DPHEVPSSLC SLPCGPGERK KMVKGVPCCW HCEACDGYRF QVDEFTCEAC PGDMRPTPNH TGCRPTPVVR LSWSSP WAA PPLLLAVLGI VATTTVVATF VRYNNTPIVR ASGRELSYVL LTGIFLIYAI TFLMVAEPGA AVCAARRLFL GLGTTLS YS ALLTKTNRIY RIFEQGKRSV TPPPFISPTS QLVITFSLTS LQVVGMIAWL GARPPHSVID YEEQRTVDPE QARGVLKC D MSDLSLIGCL GYSLLLMVTC TVYAIKARGV PETFNEAKPI GFTMYTTCII WLAFVPIFFG TAQSAEKIYI QTTTLTVSL SLSASVSLGM LYVPKTYVIL FHPEQNVQKR KRSLKATSTV AAPPKGEDAE AHKFESRAST VPRARDPPVA TLEVLFQ

UniProtKB: Metabotropic glutamate receptor 6

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Macromolecule #2: PHOSPHOSERINE

MacromoleculeName: PHOSPHOSERINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: SEP
Molecular weightTheoretical: 185.072 Da
Chemical component information

ChemComp-SEP:
PHOSPHOSERINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold Model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 244484
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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