+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37795 | ||||||||||||||||||
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Title | Cry-EM structure of cannabinoid receptor-arrestin 2 complex | ||||||||||||||||||
Map data | |||||||||||||||||||
Sample |
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Keywords | complex / MEMBRANE PROTEIN / 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 / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / cannabinoid receptor activity / angiotensin receptor binding ...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 / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / cannabinoid receptor activity / angiotensin receptor binding / negative regulation of mast cell activation / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / negative regulation of fatty acid beta-oxidation / negative regulation of dopamine secretion / positive regulation of acute inflammatory response to antigenic stimulus / regulation of feeding behavior / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of serotonin secretion / Activation of SMO / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development / negative regulation of action potential / negative regulation of interleukin-8 production / Class A/1 (Rhodopsin-like receptors) / positive regulation of blood pressure / positive regulation of fever generation / regulation of metabolic process / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / axonal fasciculation / positive regulation of intracellular signal transduction / Lysosome Vesicle Biogenesis / regulation of synaptic transmission, GABAergic / positive regulation of Rho protein signal transduction / Golgi Associated Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / stress fiber assembly / negative regulation of Notch signaling pathway / pseudopodium / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of interleukin-6 production / regulation of insulin secretion / positive regulation of receptor internalization / endocytic vesicle / GABA-ergic synapse / maternal process involved in female pregnancy / clathrin-coated pit / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / regulation of synaptic transmission, glutamatergic / cellular response to hormone stimulus / insulin-like growth factor receptor binding / activation of adenylate cyclase activity / negative regulation of blood pressure / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / 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 / Signaling by high-kinase activity BRAF mutants / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / MAP2K and MAPK activation / cytoplasmic vesicle membrane / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of neuron projection development / memory / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / Thrombin signalling through proteinase activated receptors (PARs) / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / electron transfer activity / transcription coactivator activity / periplasmic space Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Phage display vector pTDisp (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
Authors | Wang YX / Wang T / Wu LJ / Hua T / Liu ZJ | ||||||||||||||||||
Funding support | China, 5 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37795.map.gz | 57 MB | EMDB map data format | |
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Header (meta data) | emd-37795-v30.xml emd-37795.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
Images | emd_37795.png | 34.5 KB | ||
Filedesc metadata | emd-37795.cif.gz | 6.6 KB | ||
Others | emd_37795_half_map_1.map.gz emd_37795_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37795 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37795 | HTTPS FTP |
-Related structure data
Related structure data | 8wrzMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37795.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37795_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37795_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cry-EM structure of cannabinoid receptor-arrestin 2 complex
Entire | Name: Cry-EM structure of cannabinoid receptor-arrestin 2 complex |
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Components |
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-Supramolecule #1: Cry-EM structure of cannabinoid receptor-arrestin 2 complex
Supramolecule | Name: Cry-EM structure of cannabinoid receptor-arrestin 2 complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Beta-arrestin-1
Macromolecule | Name: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 44.271508 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP KEEPPHREVP ENETPVDTNL IELDTNDDDI VFEDFAR UniProtKB: Beta-arrestin-1 |
-Macromolecule #2: scfv30 light chain, scfv30 heavy chain
Macromolecule | Name: scfv30 light chain, scfv30 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Phage display vector pTDisp (others) |
Molecular weight | Theoretical: 28.693922 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQYKYVP VTFGQGTKVE IKGTTAASGS SGGSSSGAEV QLVESGGGLV Q PGGSLRLS ...String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQYKYVP VTFGQGTKVE IKGTTAASGS SGGSSSGAEV QLVESGGGLV Q PGGSLRLS CAASGFNVYS SSIHWVRQAP GKGLEWVASI SSYYGYTYYA DSVKGRFTIS ADTSKNTAYL QMNSLRAEDT AV YYCARSR QFWYSGLDYW GQGTLVTVSS A |
-Macromolecule #3: Soluble cytochrome b562,Cannabinoid receptor 1
Macromolecule | Name: Soluble cytochrome b562,Cannabinoid receptor 1 / type: protein_or_peptide / ID: 3 Details: The chimera of Cytochrome b-562, linker, and Cannabinoid receptor 1 Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 53.577543 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQA AAEQLKTTRN AYIQKYLLEV LFQGPVPADQ VNITEFYNKS LSSFKENEEN IQCGENFMDI ECFMVLNPSQ Q LAIAVLSL ...String: ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSPDSPEMKD FRHGFDILVG QIDDALKLAN EGKVKEAQA AAEQLKTTRN AYIQKYLLEV LFQGPVPADQ VNITEFYNKS LSSFKENEEN IQCGENFMDI ECFMVLNPSQ Q LAIAVLSL TLGTFTVLEN LLVLCVILHS RSLRCRPSYH FIGSLAVADL LGSVIFVYSF IDFHVFHRKD SRNVFLFKLG GV TASFTAS VGSLFLIAID RYISIHRPLA YKRIVTRPKA VVAFCLMWTI AIVIAVLPLL GWNCEKLQSV CSDIFPHIDK TYL MFWIGV VSVLLLFIVY AYMYILWKAH SHAVRMIQRG TQKSIIIHTS EDGKVQVTRP DQARMDIELA KTLVLILVVL IICW GPLLA IMVYDVFGKM NKLIKTVFAF CSMLCLLNST VNPIIYALRS KDLRHAFRSM FPSCEGTAQP LDNSMGDSDC L UniProtKB: Soluble cytochrome b562, Cannabinoid receptor 1 |
-Macromolecule #4: Vasopressin V2 receptor
Macromolecule | Name: Vasopressin V2 receptor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 2.920651 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: ARGRTPPSLG PQDESC(TPO)(TPO)A(SEP) (SEP)(SEP)LAK UniProtKB: Vasopressin V2 receptor |
-Macromolecule #5: (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanat...
Macromolecule | Name: (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 type: ligand / ID: 5 / Number of copies: 1 / Formula: 8D0 |
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Molecular weight | Theoretical: 445.658 Da |
Chemical component information | ChemComp-8D0: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 25847 / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: with 6U1N |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final 3D classification | Number classes: 4 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130058 |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8wrz: |