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- PDB-9uyp: Cryo-EM structure of a class C GPCR (Class 3) -

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Basic information

Entry
Database: PDB / ID: 9uyp
TitleCryo-EM structure of a class C GPCR (Class 3)
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 / 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
PHOSPHOSERINE / Metabotropic glutamate receptor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 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: To Be Published
Title: Cryo-EM structure of a class C GPCR (Class 3)
Authors: Lee, S.Y. / Yun, Y. / Ji, J.S. / Jeong, H. / Lee, H.H.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metabotropic glutamate receptor 6
B: 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: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46689 / Symmetry type: POINT
RefinementHighest resolution: 3.51 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411976
ELECTRON MICROSCOPYf_angle_d0.57416283
ELECTRON MICROSCOPYf_dihedral_angle_d4.2081673
ELECTRON MICROSCOPYf_chiral_restr0.0421864
ELECTRON MICROSCOPYf_plane_restr0.0042083

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