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

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Entry
Database: PDB / ID: 7ewr
TitleCryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 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


GTPase activator complex / negative regulation of voltage-gated calcium channel activity / dopamine receptor signaling pathway / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / G-protein activation / ADP signalling through P2Y purinoceptor 12 / Prostacyclin signalling through prostacyclin receptor / Activation of G protein gated Potassium channels ...GTPase activator complex / negative regulation of voltage-gated calcium channel activity / dopamine receptor signaling pathway / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / G-protein activation / ADP signalling through P2Y purinoceptor 12 / Prostacyclin signalling through prostacyclin receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through CDC42 / G alpha (z) signalling events / G beta:gamma signalling through BTK / G-protein gamma-subunit binding / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / negative regulation of signal transduction / G-protein beta-subunit binding / heterotrimeric G-protein complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G beta:gamma signalling through PI3Kgamma / G protein-coupled receptor activity / ADP signalling through P2Y purinoceptor 1 / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / GTPase activator activity / ADORA2B mediated anti-inflammatory cytokines production / presynapse / protein localization to plasma membrane / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (s) signalling events / G alpha (i) signalling events / G alpha (q) signalling events / positive regulation of GTPase activity / Extra-nuclear estrogen signaling / chaperone binding / G protein-coupled receptor signaling pathway / GTPase activity / intracellular signal transduction / signal transduction / integral component of membrane / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
G-protein coupled receptor 158/179 / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain profile. / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / RGS domain ...G-protein coupled receptor 158/179 / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain profile. / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / RGS domain / Regulator of G protein signalling domain / 7 transmembrane sweet-taste receptor of 3 GCPR / GPCR family 3, C-terminal / G-protein coupled receptors family 3 profile. / RGS domain superfamily / G-protein gamma-like domain superfamily / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein gamma-like domain / G protein gamma subunit-like motifs / GGL domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit beta-5 / Regulator of G-protein signaling 7 / Probable G-protein coupled receptor 158
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 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 governmentSSTF-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 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Data processing / Category: em_3d_reconstruction / Item: _em_3d_reconstruction.resolution

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Assembly

Deposited unit
E: Regulator of G-protein signaling 7
F: Guanine nucleotide-binding protein subunit beta-5
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)465,4736
Polymers465,4736
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area19310 Å2
ΔGint-156 kcal/mol
Surface area129450 Å2

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Components

#1: Protein Regulator of G-protein signaling 7 / RGS7


Mass: 61570.086 Da / Num. of mol.: 2
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
#2: Protein Guanine nucleotide-binding protein subunit beta-5 / Gbeta5 / Transducin beta chain 5


Mass: 43619.297 Da / Num. of mol.: 2
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
#3: 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

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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 human GPR158 in complex with RGS7-Gbeta5 in a 2:2:2 ratio
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / 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: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236504 / Symmetry type: POINT

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