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- PDB-7ewp: Cryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in ... -

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Basic information

Entry
Database: PDB / ID: 7ewp
TitleCryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio
Components
  • Guanine nucleotide-binding protein subunit beta-5
  • Probable G-protein coupled receptor 158
  • Regulator of G-protein signaling 7
KeywordsSIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / dendrite terminus / GTPase activator complex / dark adaptation / light adaption / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / cell tip / regulation of G protein-coupled receptor signaling pathway / negative regulation of G protein-coupled receptor signaling pathway ...G protein-coupled glycine receptor activity / dendrite terminus / GTPase activator complex / dark adaptation / light adaption / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / cell tip / regulation of G protein-coupled receptor signaling pathway / negative regulation of G protein-coupled receptor signaling pathway / G protein-coupled dopamine receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / parallel fiber to Purkinje cell synapse / regulation of postsynaptic membrane potential / positive regulation of GTPase activity / G-protein alpha-subunit binding / GTPase activator activity / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / transmembrane signaling receptor activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / protein-folding chaperone binding / presynaptic membrane / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / Extra-nuclear estrogen signaling / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Regulator of G-protein signalling, DHEX domain / G-protein coupled receptor 158/179 / : / : / : / Regulator of G-protein signalling DHEX domain / GPR158/179 extracellular domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin ...Regulator of G-protein signalling, DHEX domain / G-protein coupled receptor 158/179 / : / : / : / Regulator of G-protein signalling DHEX domain / GPR158/179 extracellular domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit beta-5 / Regulator of G-protein signaling 7 / Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim, Y. / Jeong, E. / Jeong, J. / Cho, Y.
Funding support3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711
National Research Foundation (NRF, Korea)2017M3A9F6029736
Other privateSSTF-BA1602-14
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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 6, 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

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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
C: Regulator of G-protein signaling 7
D: Guanine nucleotide-binding protein subunit beta-5


Theoretical massNumber of molelcules
Total (without water)360,2844
Polymers360,2844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12960 Å2
ΔGint-110 kcal/mol
Surface area96360 Å2

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Components

#1: Protein Probable G-protein coupled receptor 158


Mass: 127547.109 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
#2: Protein Regulator of G-protein signaling 7 / RGS7


Mass: 61570.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS7 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P49802
#3: Protein Guanine nucleotide-binding protein subunit beta-5 / Gbeta5 / Transducin beta chain 5


Mass: 43619.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O14775
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-RGS7-Gb5 in a 2:1:1 ratio / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
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: OTHER
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14-3260_1069: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 362999 / Symmetry type: POINT

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