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- EMDB-25126: Cryo-EM structure of GPR158 coupled to the RGS7-Gbeta5 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-25126
TitleCryo-EM structure of GPR158 coupled to the RGS7-Gbeta5 complex
Map data
SampleGPCR complexG protein-coupled receptor
  • Isoform 2 of Regulator of G-protein signaling 7
  • Guanine nucleotide-binding protein subunit beta-5
  • G-protein coupled receptor 158
  • (ligand) x 3
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events / G beta:gamma signalling through CDC42 ...Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events / G beta:gamma signalling through CDC42 / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (s) signalling events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / G-protein activation / Thrombin signalling through proteinase activated receptors (PARs) / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Activation of G protein gated Potassium channels / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (q) signalling events / negative regulation of voltage-gated calcium channel activity / G alpha (12/13) signalling events / G alpha (i) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / dopamine receptor signaling pathway / G-protein gamma-subunit binding / GTPase activating protein binding / G-protein beta-subunit binding / negative regulation of signal transduction / heterotrimeric G-protein complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G protein-coupled receptor activity / GTPase activator activity / presynapse / protein localization to plasma membrane / myelin sheath / G alpha (i) signalling events / positive regulation of GTPase activity / cell body / chaperone binding / G protein-coupled receptor signaling pathway / GTPase activity / intracellular signal transduction / protein-containing complex / 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 / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / Regulator of G protein signalling domain ...G-protein coupled receptor 158/179 / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / RGS domain superfamily / G-protein gamma-like domain superfamily / Guanine nucleotide-binding protein, beta subunit / G protein gamma subunit-like motifs / G-protein, beta subunit / G-protein gamma-like domain / 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
Regulator of G-protein signaling 7 / Guanine nucleotide-binding protein subunit beta-5 / Probable G-protein coupled receptor 158
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPatil DN / Singh S / Singh AK / Martemyanov KA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: Science / Year: 2022
Title: Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex.
Authors: Dipak N Patil / Shikha Singh / Thibaut Laboute / Timothy S Strutzenberg / Xingyu Qiu / Di Wu / Scott J Novick / Carol V Robinson / Patrick R Griffin / John F Hunt / Tina Izard / Appu K Singh ...Authors: Dipak N Patil / Shikha Singh / Thibaut Laboute / Timothy S Strutzenberg / Xingyu Qiu / Di Wu / Scott J Novick / Carol V Robinson / Patrick R Griffin / John F Hunt / Tina Izard / Appu K Singh / Kirill A Martemyanov /
Abstract: [Figure: see text].
History
DepositionOct 8, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.359
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.359
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7shf
  • Surface level: 0.359
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_25126.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 349.2 Å
0.87 Å/pix.
x 400 pix.
= 349.2 Å
0.87 Å/pix.
x 400 pix.
= 349.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.873 Å
Density
Contour LevelBy AUTHOR: 0.359 / Movie #1: 0.359
Minimum - Maximum-2.1638293 - 3.3204675
Average (Standard dev.)0.0007287576 (±0.054183245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 349.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8730.8730.873
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z349.200349.200349.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-140-140-140
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-2.1643.3200.001

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Supplemental data

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Sample components

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Entire GPCR complex

EntireName: GPCR complexG protein-coupled receptor / Number of Components: 7

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Component #1: protein, GPCR complex

ProteinName: GPCR complexG protein-coupled receptor / Recombinant expression: No
MassTheoretical: 270 kDa
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Isoform 2 of Regulator of G-protein signaling 7

ProteinName: Isoform 2 of Regulator of G-protein signaling 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.761859 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Guanine nucleotide-binding protein subunit beta-5

ProteinName: Guanine nucleotide-binding protein subunit beta-5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.778602 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, G-protein coupled receptor 158

ProteinName: G-protein coupled receptor 158 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 88.251633 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, CHOLESTEROL

LigandName: CHOLESTEROL / Number of Copies: 22 / Recombinant expression: No
MassTheoretical: 0.386654 kDa

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Component #6: ligand, (2S)-1-{[(S)-hydroxy{[(1s,2R,3R,4R,5S,6S)-2,3,4,5,6-penta...

LigandName: (2S)-1-{[(S)-hydroxy{[(1s,2R,3R,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5E,8E,11E,14E)-icosa-5,8,11,14-tetraenoate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.887128 kDa

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Component #7: ligand, 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine

LigandName: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.744034 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 8
VitrificationCryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 40 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: OTHER / Defocus: 1500.0 - 2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 151954
3D reconstructionSoftware: cryoSPARC / Resolution: 3.4 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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