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

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Basic information

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


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / cannabinoid signaling pathway / regulation of penile erection / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding ...renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / cannabinoid signaling pathway / regulation of penile erection / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / retrograde trans-synaptic signaling by endocannabinoid / cannabinoid receptor activity / angiotensin receptor binding / negative regulation of mast cell activation / negative regulation of fatty acid beta-oxidation / trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / negative regulation of dopamine secretion / positive regulation of acute inflammatory response to antigenic stimulus / TGFBR3 regulates TGF-beta signaling / negative regulation of serotonin secretion / regulation of feeding behavior / Activation of SMO / hemostasis / regulation of presynaptic cytosolic calcium ion concentration / positive regulation of systemic arterial blood pressure / 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 / arrestin family protein binding / G protein-coupled receptor internalization / regulation of metabolic process / axonal fasciculation / enzyme inhibitor activity / positive regulation of intracellular signal transduction / Lysosome Vesicle Biogenesis / regulation of synaptic transmission, GABAergic / negative regulation of NF-kappaB transcription factor activity / positive regulation of Rho protein signal transduction / Golgi Associated Vesicle Biogenesis / stress fiber assembly / negative regulation of Notch signaling pathway / positive regulation of receptor internalization / pseudopodium / negative regulation of interleukin-6 production / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / endocytic vesicle / maternal process involved in female pregnancy / activation of adenylate cyclase activity / GABA-ergic synapse / clathrin-coated pit / cellular response to hormone stimulus / positive regulation of vasoconstriction / regulation of synaptic transmission, glutamatergic / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / negative regulation of blood pressure / regulation of insulin secretion / visual perception / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / response to nutrient / response to cytokine / response to cocaine / response to nicotine / G protein-coupled receptor binding / G protein-coupled receptor activity / electron transport chain / peptide binding / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / memory / positive regulation of neuron projection development / 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 / protein transport / actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / glucose homeostasis / Clathrin-mediated endocytosis / presynaptic membrane / growth cone / G alpha (i) signalling events / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / spermatogenesis / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / mitochondrial outer membrane / response to lipopolysaccharide / periplasmic space
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
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
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Apr 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / em_entity_assembly / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _em_entity_assembly.entity_id_list / _entity_poly_seq.entity_id / _entity_poly_seq.mon_id / _entity_poly_seq.num / _entity_src_gen.entity_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_src_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / em_entity_assembly ...em_admin / em_entity_assembly / pdbx_entry_details / pdbx_modification_feature / struct
Item: _em_admin.last_update / _em_admin.title ..._em_admin.last_update / _em_admin.title / _em_entity_assembly.name / _pdbx_entry_details.has_protein_modification / _struct.title

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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

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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