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- EMDB-31360: Cryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31360
TitleCryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio
Map data
SampleGPR158-RGS7-Gb5 in a 2:1:1 ratio
  • Probable G-protein coupled receptor 158
  • Regulator of G-protein signaling 7
  • Guanine nucleotide-binding protein subunit beta-5
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKim Y / Jeong E / Jeong J / Cho Y
Funding support3 items
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, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.371
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.371
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ewp
  • Surface level: 0.371
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_31360.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 350 pix.
= 374.482 Å
1.07 Å/pix.
x 350 pix.
= 374.482 Å
1.07 Å/pix.
x 350 pix.
= 374.482 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06995 Å
Density
Contour LevelBy AUTHOR: 0.371 / Movie #1: 0.371
Minimum - Maximum-1.3871425 - 2.0562553
Average (Standard dev.)-0.001032287 (±0.038186632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 374.48248 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06994857142861.06994857142861.0699485714286
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z374.482374.482374.482
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-1.3872.056-0.001

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Supplemental data

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Additional map: Locally refined map

Fileemd_31360_additional_1.map
AnnotationLocally refined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire GPR158-RGS7-Gb5 in a 2:1:1 ratio

EntireName: GPR158-RGS7-Gb5 in a 2:1:1 ratio / Number of Components: 4

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Component #1: protein, GPR158-RGS7-Gb5 in a 2:1:1 ratio

ProteinName: GPR158-RGS7-Gb5 in a 2:1:1 ratio / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Probable G-protein coupled receptor 158

ProteinName: Probable G-protein coupled receptor 158 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 127.547109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Regulator of G-protein signaling 7

ProteinName: Regulator of G-protein signaling 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 61.570086 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Guanine nucleotide-binding protein subunit beta-5

ProteinName: Guanine nucleotide-binding protein subunit beta-5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.619297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.5 mg/mL / pH: 7.5
VitrificationCryogen Name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 50 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: DIFFRACTION
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 362999
3D reconstructionResolution: 4.3 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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