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- EMDB-37795: Cry-EM structure of cannabinoid receptor-beta-arrestin-1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37795
TitleCry-EM structure of cannabinoid receptor-beta-arrestin-1 complex
Map data
Sample
  • Complex: Cry-EM structure of cannabinoid receptor-arrestin 1 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scfv30 light chain, scfv30 heavy chain
    • Protein or peptide: Soluble cytochrome b562,Cannabinoid receptor 1
    • Protein or peptide: Vasopressin V2 receptor
  • Ligand: (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
Keywordscomplex / MEMBRANE PROTEIN / GPCR
Function / homology
Function and homology information


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 / cannabinoid signaling pathway / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding / hemostasis ...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 / cannabinoid signaling pathway / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding / hemostasis / TGFBR3 regulates TGF-beta signaling / Activation of SMO / telencephalon development / regulation of presynaptic cytosolic calcium ion concentration / negative regulation of interleukin-8 production / Class A/1 (Rhodopsin-like receptors) / G protein-coupled receptor internalization / arrestin family protein binding / axonal fasciculation / regulation of metabolic process / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of vasoconstriction / 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 / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / enzyme inhibitor activity / 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 / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor activity / MAP2K and MAPK activation / GABA-ergic synapse / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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) / presynaptic membrane / growth cone / 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 / protein ubiquitination / nuclear body / 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
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 / 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
Soluble cytochrome b562 / Cannabinoid receptor 1 / Vasopressin V2 receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human) / Phage display vector pTDisp (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWang YX / Wang T / Wu LJ / Hua T / Liu ZJ
Funding support China, 5 items
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, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37795.png

Downloads & links

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Map

FileDownload / File: emd_37795.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.169
Minimum - Maximum-0.0016821803 - 1.9413128
Average (Standard dev.)0.0011457085 (±0.024867363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37795_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37795_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cry-EM structure of cannabinoid receptor-arrestin 1 complex

EntireName: Cry-EM structure of cannabinoid receptor-arrestin 1 complex
Components
  • Complex: Cry-EM structure of cannabinoid receptor-arrestin 1 complex
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: scfv30 light chain, scfv30 heavy chain
    • Protein or peptide: Soluble cytochrome b562,Cannabinoid receptor 1
    • Protein or peptide: Vasopressin V2 receptor
  • Ligand: (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

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Supramolecule #1: Cry-EM structure of cannabinoid receptor-arrestin 1 complex

SupramoleculeName: Cry-EM structure of cannabinoid receptor-arrestin 1 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 44.271508 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: scfv30 light chain, scfv30 heavy chain

MacromoleculeName: scfv30 light chain, scfv30 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phage display vector pTDisp (others)
Molecular weightTheoretical: 28.693922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #3: Soluble cytochrome b562,Cannabinoid receptor 1

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.577543 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: Vasopressin V2 receptor

MacromoleculeName: Vasopressin V2 receptor / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.920651 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ARGRTPPSLG PQDESC(TPO)(TPO)A(SEP) (SEP)(SEP)LAK

UniProtKB: Vasopressin V2 receptor

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Macromolecule #5: (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanat...

MacromoleculeName: (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
Molecular weightTheoretical: 445.658 Da
Chemical component information

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

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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

Concentration1.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 25847 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6kpg


Details: with 6U1N
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130058
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

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

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