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- EMDB-64622: Cryo-EM structure of a class C GPCR (Class 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-64622
TitleCryo-EM structure of a class C GPCR (Class 2)
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 / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / detection of light stimulus involved in visual perception / 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 / synapse assembly ...new growing cell tip / positive regulation of calcium ion import across plasma membrane / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / detection of light stimulus involved in visual perception / 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 / synapse assembly / locomotory behavior / G protein-coupled receptor activity / retina development in camera-type eye / G alpha (i) signalling events / gene expression / chemical synaptic transmission / Golgi membrane / synapse / dendrite / endoplasmic reticulum membrane / 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: 3.27 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: To Be Published
Title: Cryo-EM structure of a class C GPCR (Class 2)
Authors: Lee SY / Yun Y / Ji JS / Jeong H / Lee HH
History
DepositionMay 15, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64622.png

Downloads & links

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Map

FileDownload / File: emd_64622.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.6148236 - 2.493876
Average (Standard dev.)-0.0005350865 (±0.039568905)
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: #1

Fileemd_64622_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64622_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 146427
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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