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- PDB-7ewl: cryo-EM structure of apo GPR158 -

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Basic information

Entry
Database: PDB / ID: 7ewl
Titlecryo-EM structure of apo GPR158
ComponentsProbable G-protein coupled receptor 158
KeywordsSIGNALING PROTEIN / Class C orphan GPCR / depression / neuronal signaling / PAS-folded GPCR / noncanonical signaling GPCR
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
Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsJeong, E. / Kim, Y. / Jeong, J. / Cho, Y.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1A6A1A10042944 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the class C orphan GPCR GPR158 in complex with RGS7-Gβ5.
Authors: Eunyoung Jeong / Yoojoong Kim / Jihong Jeong / Yunje Cho /
Abstract: GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding ...GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding domain and terminates Gαi/o protein signaling through the RGS7-Gβ5 heterodimer. Here, we report the cryo-EM structures of GPR158 alone and in complex with one or two RGS7-Gβ5 heterodimers. GPR158 dimerizes through Per-Arnt-Sim-fold extracellular and transmembrane (TM) domains connected by an epidermal growth factor-like linker. The TM domain (TMD) reflects both inactive and active states of other class C GPCRs: a compact intracellular TMD, conformations of the two intracellular loops (ICLs) and the TMD interface formed by TM4/5. The ICL2, ICL3, TM3, and first helix of the cytoplasmic coiled-coil provide a platform for the DHEX domain of one RGS7 and the second helix recruits another RGS7. The unique features of the RGS7-binding site underlie the selectivity of GPR158 for RGS7.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Probable G-protein coupled receptor 158
B: Probable G-protein coupled receptor 158


Theoretical massNumber of molelcules
Total (without water)154,9252
Polymers154,9252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3510 Å2
ΔGint-39 kcal/mol
Surface area57580 Å2

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Components

#1: Protein Probable G-protein coupled receptor 158


Mass: 77462.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR158 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q5T848
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: GPR158 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 200 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
SpecimenConc.: 12.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 425819 / Num. of class averages: 1 / Symmetry type: POINT

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