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- EMDB-37849: Cryo-EM structure of CB1-beta-arrestin1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37849
TitleCryo-EM structure of CB1-beta-arrestin1 complex
Map data
Sample
  • Complex: Cryo-EM structure of human cannabinoid receptor 1 with effector protein
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
    • Protein or peptide: Cannabinoid receptor 1,Vasopressin V2 receptor
  • Ligand: methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate
Keywordscannabinoid receptor / arrestin / biased signal / class A GPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / MAP2K and MAPK activation / Vasopressin-like receptors / cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / 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) / MAP2K and MAPK activation / Vasopressin-like receptors / cannabinoid signaling pathway / regulation of penile erection / retrograde trans-synaptic signaling by endocannabinoid / 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 / clathrin heavy chain binding / negative regulation of dopamine secretion / Ub-specific processing proteases / positive regulation of acute inflammatory response to antigenic stimulus / regulation of feeding behavior / clathrin coat of coated pit / negative regulation of serotonin secretion / regulation of presynaptic cytosolic calcium ion concentration / hemostasis / desensitization of G protein-coupled receptor signaling pathway / telencephalon development / Cargo recognition for clathrin-mediated endocytosis / negative regulation of action potential / positive regulation of systemic arterial blood pressure / inositol hexakisphosphate binding / Class A/1 (Rhodopsin-like receptors) / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / positive regulation of blood pressure / 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 / phosphatidylinositol-3,4,5-trisphosphate binding / regulation of insulin secretion / positive regulation of receptor internalization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / endocytic vesicle / GABA-ergic synapse / small molecule binding / 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 / visual perception / negative regulation of blood pressure / response to nutrient / response to cocaine / response to cytokine / G protein-coupled receptor binding / G protein-coupled receptor activity / peptide binding / response to nicotine / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / receptor internalization / memory / positive regulation of neuron projection development / Vasopressin regulates renal water homeostasis via Aquaporins / protein transport / actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / glucose homeostasis / Clathrin-mediated endocytosis / presynaptic membrane / G alpha (i) signalling events / growth cone / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / spermatogenesis / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / 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 / Vasopressin receptor / Cannabinoid receptor type 1 / Cannabinoid receptor family / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain ...Vasopressin V2 receptor / Vasopressin receptor / Cannabinoid receptor type 1 / 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
Beta-arrestin-1 / Cannabinoid receptor 1 / Vasopressin V2 receptor
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiao Y / Zhang H / Shen Q / Cai C
Funding support China, 1 items
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, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37849.png

Downloads & links

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Map

FileDownload / File: emd_37849.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.93 Å
Density
Contour LevelBy AUTHOR: 0.0035
Minimum - Maximum-0.025322681 - 0.046268616
Average (Standard dev.)0.000000027926436 (±0.0009535786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37849_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37849_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human cannabinoid receptor 1 with effector p...

EntireName: Cryo-EM structure of human cannabinoid receptor 1 with effector protein
Components
  • Complex: Cryo-EM structure of human cannabinoid receptor 1 with effector protein
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30 heavy chain
    • Protein or peptide: Fab30 light chain
    • Protein or peptide: Cannabinoid receptor 1,Vasopressin V2 receptor
  • Ligand: methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate

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Supramolecule #1: Cryo-EM structure of human cannabinoid receptor 1 with effector p...

SupramoleculeName: Cryo-EM structure of human cannabinoid receptor 1 with effector protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: MDMB-Fubinaca, cannabinoid receptor 1, arrestin2, Fab30
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 44.135273 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVEPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI EKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP EHETPVDTNL IELDTNDDDA AAEDFAR

UniProtKB: Beta-arrestin-1

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Macromolecule #2: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.650502 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHHH

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Macromolecule #3: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: Cannabinoid receptor 1,Vasopressin V2 receptor

MacromoleculeName: Cannabinoid receptor 1,Vasopressin V2 receptor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.310129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKSILDGLAD TTFRTITTDL LYVGSNDIQY EDIKGDMASK LGYFPQKFPL TSFRGSPFQE KMTAGDNPQL VPADQVNITE FYNKSLSSF KENEENIQCG ENFMDIECFM VLNPSQQLAI AVLSLTLGTF TVLENLLVLC VILHSRSLRC RPSYHFIGSL A VADLLGSV ...String:
MKSILDGLAD TTFRTITTDL LYVGSNDIQY EDIKGDMASK LGYFPQKFPL TSFRGSPFQE KMTAGDNPQL VPADQVNITE FYNKSLSSF KENEENIQCG ENFMDIECFM VLNPSQQLAI AVLSLTLGTF TVLENLLVLC VILHSRSLRC RPSYHFIGSL A VADLLGSV IFVYSFIDFH VFHRKDSRNV FLFKLGGVTA SFTASVGSLF LTAIDRYISI HRPLAYKRIV TRPKAVVAFC LM WTIAIVI AVLPLLGWNC EKLQSVCSDI FPHIDETYLM FWIGVTSVLL LFIVYAYMYI LWKAHSHAVR MIQRGTQKSI IIH TSEDGK VQVTRPDQAR MDIRLAKTLV LILVVLIICW GPLLAIMVYD VFGKMNKLIK TVFAFCSMLC LLNSTVNPII YALR SKDLR HAFRSMFPCA RGRTPPSLGP QDE(SEP)C(TPO)(TPO)A(SEP)(SEP) (SEP)LAKDTSS

UniProtKB: Cannabinoid receptor 1, Vasopressin V2 receptor

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Macromolecule #5: methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-me...

MacromoleculeName: methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate
type: ligand / ID: 5 / Number of copies: 1 / Formula: KCA
Molecular weightTheoretical: 397.443 Da
Chemical component information

ChemComp-KCA:
methyl N-{1-[(4-fluorophenyl)methyl]-1H-indazole-3-carbonyl}-3-methyl-L-valinate / agonist*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110196
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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