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- PDB-7shf: Cryo-EM structure of GPR158 coupled to the RGS7-Gbeta5 complex -

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Basic information

Entry
Database: PDB / ID: 7shf
TitleCryo-EM structure of GPR158 coupled to the RGS7-Gbeta5 complex
Components
  • G-protein coupled receptor 158
  • Guanine nucleotide-binding protein subunit beta-5
  • Isoform 2 of Regulator of G-protein signaling 7
KeywordsSIGNALING PROTEIN / Receptor / complex
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / Inactivation, recovery and regulation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK ...G protein-coupled glycine receptor activity / Inactivation, recovery and regulation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Prostacyclin signalling through prostacyclin receptor / G alpha (z) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / light adaption / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / dark adaptation / Thromboxane signalling through TP receptor / G-protein gamma-subunit binding / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Ca2+ pathway / G alpha (s) signalling events / G alpha (q) signalling events / Extra-nuclear estrogen signaling / negative regulation of voltage-gated calcium channel activity / G alpha (12/13) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (i) signalling events / GPER1 signaling / negative regulation of G protein-coupled receptor signaling pathway / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of potassium ion transmembrane transport / ADP signalling through P2Y purinoceptor 1 / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / GTPase activating protein binding / dopamine receptor signaling pathway / regulation of synapse organization / enzyme activator activity / G-protein alpha-subunit binding / response to amphetamine / GTPase activator activity / cell projection / G protein-coupled receptor activity / protein localization to plasma membrane / brain development / cognition / positive regulation of GTPase activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / transmembrane signaling receptor activity / presynapse / presynaptic membrane / myelin sheath / nuclear envelope / cell body / G alpha (i) signalling events / protein-folding chaperone binding / postsynaptic membrane / response to ethanol / neuron projection / intracellular signal transduction / G protein-coupled receptor signaling pathway / GTPase activity / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / G-protein coupled receptor 158/179 / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain ...: / : / G-protein coupled receptor 158/179 / Regulator of G-protein signalling, DHEX domain / Regulator of G-protein signalling DHEX domain / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
CHOLESTEROL / Chem-EIJ / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Regulator of G-protein signaling 7 / Guanine nucleotide-binding protein subunit beta-5 / Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPatil, D.N. / Singh, S. / Singh, A.K. / Martemyanov, K.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: Science / Year: 2022
Title: Cryo-EM structure of human GPR158 receptor coupled to the RGS7-Gβ5 signaling complex.
Authors: Dipak N Patil / Shikha Singh / Thibaut Laboute / Timothy S Strutzenberg / Xingyu Qiu / Di Wu / Scott J Novick / Carol V Robinson / Patrick R Griffin / John F Hunt / Tina Izard / Appu K Singh ...Authors: Dipak N Patil / Shikha Singh / Thibaut Laboute / Timothy S Strutzenberg / Xingyu Qiu / Di Wu / Scott J Novick / Carol V Robinson / Patrick R Griffin / John F Hunt / Tina Izard / Appu K Singh / Kirill A Martemyanov /
Abstract: GPR158 is an orphan G protein–coupled receptor (GPCR) highly expressed in the brain, where it controls synapse formation and function. GPR158 has also been implicated in depression, carcinogenesis, ...GPR158 is an orphan G protein–coupled receptor (GPCR) highly expressed in the brain, where it controls synapse formation and function. GPR158 has also been implicated in depression, carcinogenesis, and cognition. However, the structural organization and signaling mechanisms of GPR158 are largely unknown. We used single-particle cryo–electron microscopy (cryo-EM) to determine the structures of human GPR158 alone and bound to an RGS signaling complex. The structures reveal a homodimeric organization stabilized by a pair of phospholipids and the presence of an extracellular Cache domain, an unusual ligand-binding domain in GPCRs. We further demonstrate the structural basis of GPR158 coupling to RGS7-Gβ5. Together, these results provide insights into the unusual biology of orphan receptors and the formation of GPCR-RGS complexes.
History
DepositionOct 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 2.0Dec 29, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Data processing / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / em_ctf_correction / em_imaging / em_single_particle_entity / em_software / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_torsion / struct / struct_asym / struct_conf / struct_ref / struct_ref_seq
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _em_ctf_correction.type / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _em_software.name / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct.title / _struct_asym.entity_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
C: Isoform 2 of Regulator of G-protein signaling 7
D: Guanine nucleotide-binding protein subunit beta-5
B: G-protein coupled receptor 158
A: G-protein coupled receptor 158
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,18128
Polymers270,0444
Non-polymers10,13824
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 4 molecules CDBA

#1: Protein Isoform 2 of Regulator of G-protein signaling 7 / RGS7


Mass: 54761.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGS7 / Production host: Homo sapiens (human) / References: UniProt: P49802
#2: Protein Guanine nucleotide-binding protein subunit beta-5 / Gbeta5 / Transducin beta chain 5


Mass: 38778.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnb5 / Production host: Homo sapiens (human) / References: UniProt: P62881
#3: Protein G-protein coupled receptor 158 / GPR


Mass: 88251.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR158, KIAA1136 / Production host: Homo sapiens (human) / References: UniProt: Q5T848

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Non-polymers , 3 types, 24 molecules

#4: Chemical...
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-EIJ / (2S)-1-{[(S)-hydroxy{[(1s,2R,3R,4R,5S,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5E,8E,11E,14E)-icosa-5,8,11,14-tetraenoate


Mass: 887.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H83O13P
#6: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM

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Details

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: GPCR complexG protein-coupled receptor / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.270 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenConc.: 0.3 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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151954 / Symmetry type: POINT

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