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- PDB-9vor: Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20 -

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Basic information

Entry
Database: PDB / ID: 9vor
TitleCryo-EM Structure of Human GPR158 Bound to Nanobody Nb20
Components
  • Metabotropic glycine receptor
  • Nb20
KeywordsMEMBRANE PROTEIN / GPCR / orphan receptor / nanobody / RGS proteins / signalling receptor
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition ...G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition / transmembrane signaling receptor activity / presynaptic membrane / postsynaptic membrane / G protein-coupled receptor signaling pathway / nucleus / plasma membrane
Similarity search - Function
G-protein coupled receptor 158/179 / : / GPR158/179 extracellular domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
CHOLESTEROL / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsLaboute, T. / Zucca, S. / Sial, M. / Sharma, M. / Brunori, G. / Singh, S. / Singh, A. / Martemyanov, K.
Funding support United States, India, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)MH105482 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY034339 United States
Indian Council of Medical ResearchNeuro/2022-NCD-I India
Department of Biotechnology (DBT, India)Neuro/2022-NCD-I India
CitationJournal: To Be Published
Title: Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20
Authors: Laboute, T. / Zucca, S. / Sial, M. / Sharma, M. / Brunori, G. / Singh, S. / Singh, A. / Martemyanov, K.
History
DepositionJul 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 31, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Metabotropic glycine receptor
B: Metabotropic glycine receptor
C: Nb20
E: Nb20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,26126
Polymers209,9484
Non-polymers9,31322
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 glycine receptor / mGlyR / G-protein coupled receptor 158


Mass: 88251.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR158, KIAA1136 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5T848
#2: Antibody Nb20


Mass: 16722.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#5: Chemical ChemComp-PIE / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol


Mass: 836.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H80O13P / 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: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1GPR158 complexed with Nb20COMPLEX#1-#20RECOMBINANT
2GPR158COMPLEX#11RECOMBINANT
3NanobodyCOMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 8
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 40

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 121523 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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