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- PDB-8wu1: Cryo-EM structure of CB1-beta-arrestin1 complex -

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Basic information

Entry
Database: PDB / ID: 8wu1
TitleCryo-EM structure of CB1-beta-arrestin1 complex
Components
  • Beta-arrestin-1Arrestin
  • Cannabinoid receptor 1,Vasopressin V2 receptor
  • Fab30 heavy chain
  • Fab30 light chain
KeywordsMEMBRANE PROTEIN / cannabinoid receptor / arrestin / biased signal / class A GPCR
Function / homology
Function and homology information


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / MAP2K and MAPK activation / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / Activation of SMO ...renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / MAP2K and MAPK activation / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / Activation of SMO / Golgi Associated Vesicle Biogenesis / cannabinoid receptor activity / Lysosome Vesicle Biogenesis / negative regulation of mast cell activation / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / AP-2 adaptor complex binding / negative regulation of fatty acid beta-oxidation / negative regulation of dopamine secretion / clathrin heavy chain binding / positive regulation of acute inflammatory response to antigenic stimulus / clathrin coat of coated pit / Ub-specific processing proteases / regulation of feeding behavior / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of serotonin secretion / desensitization of G protein-coupled receptor signaling pathway / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development / Cargo recognition for clathrin-mediated endocytosis / negative regulation of action potential / inositol hexakisphosphate binding / Class A/1 (Rhodopsin-like receptors) / Clathrin-mediated endocytosis / positive regulation of blood pressure / clathrin-dependent endocytosis / positive regulation of fever generation / regulation of metabolic process / G protein-coupled receptor internalization / acetylcholine receptor binding / axonal fasciculation / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / positive regulation of intracellular signal transduction / regulation of synaptic transmission, GABAergic / clathrin binding / negative regulation of Notch signaling pathway / pseudopodium / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / phosphatidylinositol-3,4,5-trisphosphate binding / small molecule binding / regulation of insulin secretion / positive regulation of receptor internalization / endocytic vesicle / GABA-ergic synapse / maternal process involved in female pregnancy / positive regulation of vasoconstriction / regulation of synaptic transmission, glutamatergic / cellular response to hormone stimulus / activation of adenylate cyclase activity / negative regulation of blood pressure / visual perception / response to nutrient / response to cocaine / response to nicotine / G protein-coupled receptor binding / response to cytokine / G protein-coupled receptor activity / peptide binding / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of neuron projection development / receptor internalization / memory / Vasopressin regulates renal water homeostasis via Aquaporins / actin cytoskeleton / protein transport / Cargo recognition for clathrin-mediated endocytosis / glucose homeostasis / presynaptic membrane / Clathrin-mediated endocytosis / G alpha (i) signalling events / growth cone / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (s) signalling events / spermatogenesis / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / endosome / positive regulation of protein phosphorylation / positive regulation of apoptotic process / membrane raft / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / glutamatergic synapse
Similarity search - Function
Vasopressin V2 receptor / Cannabinoid receptor type 1 / Vasopressin receptor / Cannabinoid receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Vasopressin V2 receptor / Cannabinoid receptor type 1 / 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 / 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-KCA / Beta-arrestin-1 / Cannabinoid receptor 1 / Vasopressin V2 receptor
Similarity search - Component
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiao, Y. / Zhang, H. / Shen, Q. / Cai, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: Cryo-EM structure of CB1-beta-arrestin1 complex
Authors: Liao, Y. / Zhang, H. / Shen, Q. / Cai, C.
History
DepositionOct 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-arrestin-1
H: Fab30 heavy chain
L: Fab30 light chain
R: Cannabinoid receptor 1,Vasopressin V2 receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,9285
Polymers143,5314
Non-polymers3971
Water0
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 / Arrestin


Mass: 44135.273 Da / Num. of mol.: 1 / Mutation: R169E, I386A, V387A, F388A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P17870
#2: Antibody Fab30 heavy chain


Mass: 25650.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Protein Cannabinoid receptor 1,Vasopressin V2 receptor


Mass: 50310.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNR1, AVPR2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21554, UniProt: P30518
#5: Chemical ChemComp-KCA / methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate / MDMB-FUBINACA


Mass: 397.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24FN3O3 / Comment: agonist*YM
Has ligand of interestN

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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 cannabinoid receptor 1 with effector protein
Type: COMPLEX
Details: MDMB-Fubinaca, cannabinoid receptor 1, arrestin2, Fab30
Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Bos taurus (cattle)9913
21Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Spodoptera frugiperda (fall armyworm)7108
21Escherichia coli BL21(DE3) (bacteria)469008
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELDBright-field microscopy / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110196 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047437
ELECTRON MICROSCOPYf_angle_d0.85810216
ELECTRON MICROSCOPYf_dihedral_angle_d4.1874360
ELECTRON MICROSCOPYf_chiral_restr0.0411245
ELECTRON MICROSCOPYf_plane_restr0.0041267

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