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- PDB-8wrz: Cry-EM structure of cannabinoid receptor-beta-arrestin-1 complex -

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Entry
Database: PDB / ID: 8wrz
TitleCry-EM structure of cannabinoid receptor-beta-arrestin-1 complex
Components
  • Beta-arrestin-1
  • Soluble cytochrome b562,Cannabinoid receptor 1
  • Vasopressin V2 receptor
  • scfv30 light chain, scfv30 heavy chain
KeywordsMEMBRANE PROTEIN / complex / GPCR
Function / homology
Function and homology information


cannabinoid signaling pathway / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling ...cannabinoid signaling pathway / renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / hemostasis / Activation of SMO / telencephalon development / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of interleukin-8 production / Class A/1 (Rhodopsin-like receptors) / arrestin family protein binding / G protein-coupled receptor internalization / axonal fasciculation / regulation of metabolic process / Lysosome Vesicle Biogenesis / : / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of vasoconstriction / positive regulation of Rho protein signal transduction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / endocytic vesicle / negative regulation of Notch signaling pathway / enzyme inhibitor activity / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / response to cytokine / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / clathrin-coated endocytic vesicle membrane / electron transport chain / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor binding / MAP2K and MAPK activation / G protein-coupled receptor activity / GABA-ergic synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / glucose homeostasis / protein transport / actin cytoskeleton / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / growth cone / presynaptic membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (i) signalling events / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / transcription coactivator activity / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / endosome / Ub-specific processing proteases / nuclear body / protein ubiquitination / G protein-coupled receptor signaling pathway / membrane raft / iron ion binding / Golgi membrane / negative regulation of cell population proliferation / lysosomal membrane / positive regulation of cell population proliferation / heme binding / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum
Similarity search - Function
Cannabinoid receptor type 1 / Vasopressin V2 receptor / Vasopressin receptor / Cannabinoid receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Cannabinoid receptor type 1 / Vasopressin V2 receptor / Vasopressin receptor / Cannabinoid receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Chem-8D0 / Soluble cytochrome b562 / Cannabinoid receptor 1 / Vasopressin V2 receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Phage display vector pTDisp (others)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang, Y.X. / Wang, T. / Wu, L.J. / Hua, T. / Liu, Z.J.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953202 China
Chinese Academy of SciencesXDB37030104 China
National Science Foundation (NSF, China)32022038 China
National Natural Science Foundation of China (NSFC)31930060 China
National Natural Science Foundation of China (NSFC)31870744 China
CitationJournal: Protein Cell / Year: 2024
Title: Cryo-EM structure of cannabinoid receptor CB1-β-arrestin complex.
Authors: Yuxia Wang / Lijie Wu / Tian Wang / Junlin Liu / Fei Li / Longquan Jiang / Zhongbo Fan / Yanan Yu / Na Chen / Qianqian Sun / Qiwen Tan / Tian Hua / Zhi-Jie Liu /
History
DepositionOct 16, 2023Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
L: scfv30 light chain, scfv30 heavy chain
R: Soluble cytochrome b562,Cannabinoid receptor 1
V: Vasopressin V2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9095
Polymers129,4644
Non-polymers4461
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Beta-arrestin-1


Mass: 44271.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49407
#2: Antibody scfv30 light chain, scfv30 heavy chain


Mass: 28693.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage display vector pTDisp (others) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein Soluble cytochrome b562,Cannabinoid receptor 1


Mass: 53577.543 Da / Num. of mol.: 1 / Mutation: M29W, H124I, T210I, E273K, T283V, R340E
Source method: isolated from a genetically manipulated source
Details: The chimera of Cytochrome b-562, linker, and Cannabinoid receptor 1
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, CNR1 / Production host: Homo sapiens (human) / Strain (production host): CNR1 / References: UniProt: P0ABE7, UniProt: P21554
#4: Protein/peptide Vasopressin V2 receptor


Mass: 2920.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AVPR2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): CNR / References: UniProt: P30518
#5: Chemical ChemComp-8D0 / (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol


Mass: 445.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H39NO3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Cry-EM structure of cannabinoid receptor-arrestin 1 complex
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 25847

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130058 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047069
ELECTRON MICROSCOPYf_angle_d0.7849602
ELECTRON MICROSCOPYf_dihedral_angle_d7.704980
ELECTRON MICROSCOPYf_chiral_restr0.0471106
ELECTRON MICROSCOPYf_plane_restr0.0061186

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