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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


Presynaptic function of Kainate receptors / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PLC beta / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events / G beta:gamma signalling through CDC42 ...Presynaptic function of Kainate receptors / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PLC beta / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Glucagon-type ligand receptors / G alpha (z) signalling events / G beta:gamma signalling through CDC42 / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (s) signalling events / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / G-protein activation / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (q) signalling events / negative regulation of voltage-gated calcium channel activity / G alpha (12/13) signalling events / G alpha (i) signalling events / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADP signalling through P2Y purinoceptor 1 / dopamine receptor signaling pathway / G-protein gamma-subunit binding / GTPase activating protein binding / G-protein beta-subunit binding / negative regulation of signal transduction / heterotrimeric G-protein complex / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G protein-coupled receptor activity / GTPase activator activity / presynapse / protein localization to plasma membrane / myelin sheath / G alpha (i) signalling events / positive regulation of GTPase activity / cell body / chaperone binding / G protein-coupled receptor signaling pathway / GTPase activity / intracellular signal transduction / protein-containing complex / integral component of membrane / plasma membrane / nucleus / 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 / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / Regulator of G protein signalling domain ...G-protein coupled receptor 158/179 / Regulator of G-protein signalling DHEX domain / Regulator of G-protein signalling, DHEX domain / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain / Regulator of G protein signaling domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / RGS domain superfamily / G-protein gamma-like domain superfamily / Guanine nucleotide-binding protein, beta subunit / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein subunit beta-5 / Regulator of G-protein signaling 7 / CHOLESTEROL / Chem-EIJ / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Probable G-protein coupled receptor 158
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: [Figure: see text].
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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