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- EMDB-0339: Cannabinoid Receptor 1-G Protein Complex -

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Entry
Database: EMDB / ID: 0339
TitleCannabinoid Receptor 1-G Protein Complex
Map dataStructure of a Signaling Cannabinoid Receptor 1-G Protein Complex
SampleCannabinoid Receptor 1-G Protein Complex
  • (Guanine nucleotide-binding protein ...) x 3
  • Cannabinoid receptor 1
  • scFv16
  • (ligand) x 2
Function / homologyGlucagon-type ligand receptors / GPCR, rhodopsin-like, 7TM / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats signature. / G-protein coupled receptors family 1 signature. / GGL domain / Vasopressin regulates renal water homeostasis via Aquaporins / WD domain, G-beta repeat / 7 transmembrane receptor (rhodopsin family) / WD40-repeat-containing domain superfamily ...Glucagon-type ligand receptors / GPCR, rhodopsin-like, 7TM / G-protein gamma subunit domain profile. / Trp-Asp (WD) repeats signature. / G-protein coupled receptors family 1 signature. / GGL domain / Vasopressin regulates renal water homeostasis via Aquaporins / WD domain, G-beta repeat / 7 transmembrane receptor (rhodopsin family) / WD40-repeat-containing domain superfamily / G-protein gamma-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / G-protein beta WD-40 repeat / WD40 repeat, conserved site / WD40-repeat-containing domain / Guanine nucleotide-binding protein, beta subunit / G-protein coupled receptors family 1 profile. / WD40/YVTN repeat-like-containing domain superfamily / G-protein gamma-like domain / G protein alpha subunit, helical insertion / Cannabinoid receptor family / G-protein, gamma subunit / WD40 repeat / G-protein, beta subunit / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / Cannabinoid receptor type 1 / G protein-coupled receptor, rhodopsin-like / Thromboxane signalling through TP receptor / Regulation of insulin secretion / Trp-Asp (WD) repeats profile. / G-protein alpha subunit / Trp-Asp (WD) repeats circular profile. / G beta:gamma signalling through PI3Kgamma / G alpha (q) signalling events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / PLC beta mediated events / G alpha (s) signalling events / Presynaptic function of Kainate receptors / Ca2+ pathway / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / ADP signalling through P2Y purinoceptor 1 / Thrombin signalling through proteinase activated receptors (PARs) / Adrenaline,noradrenaline inhibits insulin secretion / Prostacyclin signalling through prostacyclin receptor / ADP signalling through P2Y purinoceptor 12 / G alpha (12/13) signalling events / Olfactory Signaling Pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Class A/1 (Rhodopsin-like receptors) / Inactivation, recovery and regulation of the phototransduction cascade / Activation of the phototransduction cascade / G alpha (i) signalling events / G-protein activation / Adenylate cyclase inhibitory pathway / G alpha (z) signalling events / Glucagon signaling in metabolic regulation / Activation of G protein gated Potassium channels / G beta:gamma signalling through PLC beta / retrograde trans-synaptic signaling by endocannabinoid / regulation of penile erection / cannabinoid signaling pathway / cannabinoid receptor activity / negative regulation of dopamine secretion / voltage-gated calcium channel activity involved in positive regulation of presynaptic cytosolic calcium levels / negative regulation of mast cell activation / regulation of feeding behavior / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / negative regulation of nitric-oxide synthase activity / negative regulation of fatty acid beta-oxidation / negative regulation of action potential / cellular response to catecholamine stimulus / regulation of cAMP-mediated signaling / integral component of mitochondrial membrane / G protein-coupled serotonin receptor binding / cardiac muscle cell apoptotic process / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of protein localization to cell cortex / G protein-coupled acetylcholine receptor signaling pathway / protein heterotrimerization / sensory perception of taste / alkylglycerophosphoethanolamine phosphodiesterase activity / G-protein beta-subunit binding / adenylate cyclase-activating dopamine receptor signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / rhodopsin mediated signaling pathway / photoreceptor outer segment membrane / cell cortex region / positive regulation of blood pressure / positive regulation of fever generation / G-protein beta/gamma-subunit complex binding / spectrin binding / photoreceptor disc membrane / regulation of synaptic transmission, GABAergic / regulation of mitotic spindle organization / heterotrimeric G-protein complex / cellular response to forskolin / Wnt signaling pathway, calcium modulating pathway / axonal fasciculation / GABA-ergic synapse
Function and homology information
SourceHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / 3 Å resolution
AuthorsKrishna Kumar K / Shalev-Benami M / Hu H / Weis WI / Kobilka BK / Skiniotis G
CitationJournal: Cell / Year: 2019
Title: Structure of a Signaling Cannabinoid Receptor 1-G Protein Complex.
Authors: Kaavya Krishna Kumar / Moran Shalev-Benami / Michael J Robertson / Hongli Hu / Samuel D Banister / Scott A Hollingsworth / Naomi R Latorraca / Hideaki E Kato / Daniel Hilger / Shoji Maeda / William I Weis / David L Farrens / Ron O Dror / Sanjay V Malhotra / Brian K Kobilka / Georgios Skiniotis
Abstract: Cannabis elicits its mood-enhancing and analgesic effects through the cannabinoid receptor 1 (CB1), a G protein-coupled receptor (GPCR) that signals primarily through the adenylyl cyclase-inhibiting ...Cannabis elicits its mood-enhancing and analgesic effects through the cannabinoid receptor 1 (CB1), a G protein-coupled receptor (GPCR) that signals primarily through the adenylyl cyclase-inhibiting heterotrimeric G protein G. Activation of CB1-G signaling pathways holds potential for treating a number of neurological disorders and is thus crucial to understand the mechanism of G activation by CB1. Here, we present the structure of the CB1-G signaling complex bound to the highly potent agonist MDMB-Fubinaca (FUB), a recently emerged illicit synthetic cannabinoid infused in street drugs that have been associated with numerous overdoses and fatalities. The structure illustrates how FUB stabilizes the receptor in an active state to facilitate nucleotide exchange in G. The results compose the structural framework to explain CB1 activation by different classes of ligands and provide insights into the G protein coupling and selectivity mechanisms adopted by the receptor.
Validation ReportPDB-ID: 6n4b

SummaryFull reportAbout validation report
DateDeposition: Nov 18, 2018 / Header (metadata) release: Jan 23, 2019 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6n4b
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0339.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
0.86 Å/pix.
= 206.4 Å
240 pix
0.86 Å/pix.
= 206.4 Å
240 pix
0.86 Å/pix.
= 206.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour Level:0.085 (by author), 0.12 (movie #1):
Minimum - Maximum-0.5023643 - 0.91575676
Average (Standard dev.)-0.0012226657 (0.029975073)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 206.40001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z206.400206.400206.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.5020.916-0.001

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Supplemental data

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Sample components

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Entire Cannabinoid Receptor 1-G Protein Complex

EntireName: Cannabinoid Receptor 1-G Protein Complex / Number of components: 8

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Component #1: protein, Cannabinoid Receptor 1-G Protein Complex

ProteinName: Cannabinoid Receptor 1-G Protein Complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #2: protein, Guanine nucleotide-binding protein G(i) subunit alpha-1

ProteinName: Guanine nucleotide-binding protein G(i) subunit alpha-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.415031 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(T) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.671102 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #4: protein, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subuni...

ProteinName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.861143 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, Cannabinoid receptor 1

ProteinName: Cannabinoid receptor 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.678535 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #6: protein, scFv16

ProteinName: scFv16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.784896 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #7: ligand, methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbon...

LigandName: methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.397443 kDa

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Component #8: ligand, CHOLESTEROL

LigandName: CHOLESTEROL / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.386654 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 177787
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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