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- PDB-7xxh: Cryo-EM structure of the purinergic receptor P2Y1R in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7xxh
TitleCryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • P2Y purinoceptor 1
  • scfv16
KeywordsMEMBRANE PROTEIN / G protein-coupled receptor / purinergic receptor / P2Y1R / ligand binding / signal transduction
Function / homology
Function and homology information


G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection / negative regulation of norepinephrine secretion ...G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection / negative regulation of norepinephrine secretion / A1 adenosine receptor binding / glial cell migration / regulation of presynaptic cytosolic calcium ion concentration / G protein-coupled adenosine receptor signaling pathway / positive regulation of hormone secretion / signal transduction involved in regulation of gene expression / response to growth factor / cellular response to ATP / eating behavior / regulation of synaptic vesicle exocytosis / monoatomic ion transport / presynaptic active zone membrane / response to mechanical stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / blood vessel diameter maintenance / establishment of localization in cell / protein localization to plasma membrane / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / platelet activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP binding / Sensory perception of sweet, bitter, and umami (glutamate) taste / cilium / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / signaling receptor activity / regulation of cell shape / G alpha (i) signalling events / cell body / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / G alpha (s) signalling events / scaffold protein binding / G alpha (q) signalling events / basolateral plasma membrane / postsynaptic membrane / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / postsynaptic density / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / apical plasma membrane / G protein-coupled receptor signaling pathway / protein heterodimerization activity / lysosomal membrane / GTPase activity / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / cell surface
Similarity search - Function
P2Y purinoceptor 1 / G-protein, gamma subunit / G-protein gamma subunit domain 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 ...P2Y purinoceptor 1 / G-protein, gamma subunit / G-protein gamma subunit domain 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 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) / G-protein beta WD-40 repeat / 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 / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-6AD / P2Y purinoceptor 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan, Q. / Li, B. / Han, S. / Zhao, Q. / Wu, B.
Funding support China, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
National Science Foundation (NSF, China)82121005 China
Ministry of Science and Technology (MoST, China)2018YFA0507000 China
Chinese Academy of SciencesXDB37030100 China
Chinese Academy of SciencesJCYJ-SHFY-2021-008 China
CitationJournal: Protein Cell / Year: 2023
Title: Structural insights into signal transduction of the purinergic receptors P2Y1R and P2Y12R.
Authors: Beibei Li / Shuo Han / Mu Wang / Yu Yu / Limin Ma / Xiaojing Chu / Qiuxiang Tan / Qiang Zhao / Beili Wu /
History
DepositionMay 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: P2Y purinoceptor 1
A: Guanine nucleotide-binding protein G(11) subunit alpha
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H: scfv16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,6006
Polymers160,1265
Non-polymers4731
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, single particle
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#2: Protein Guanine nucleotide-binding protein G(11) subunit alpha


Mass: 41385.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1


Mass: 38245.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Protein / Antibody / Non-polymers , 3 types, 3 molecules RH

#1: Protein P2Y purinoceptor 1 / P2Y1 / ADP receptor / Purinergic receptor


Mass: 46296.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: P2RY1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P47900
#5: Antibody scfv16


Mass: 26337.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#6: Chemical ChemComp-6AD / 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) / 2-methylthio-adenosine-5'-diphosphate


Mass: 473.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O10P2S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16
Type: COMPLEX / Details: scf16 was recombinantly expressed in sf9 cells / Entity ID: #2-#5 / Source: RECOMBINANT
Molecular weightValue: 10 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer componentConc.: 2.0 mg/ml / Name: sodium chloride / Formula: 150mM
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: blot for 1s

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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: 1500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Image recordingAverage exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 9856 / Details: Images were collected in movie-mode

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Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4Gctfv1.06CTF correction
12RELION3classification
Image processingDetails: The selected images were 20eV using GIF-Quantum LS Imaging energy filter
CTF correctionType: NONE
Particle selectionNum. of particles selected: 6184568
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659399 / Symmetry type: POINT
Atomic model buildingB value: 43.86 / Space: REAL
Atomic model buildingPDB-ID: 4NXW

4nxw


Accession code: 4NXW / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00199040
ELECTRON MICROSCOPYf_angle_d0.487212293
ELECTRON MICROSCOPYf_chiral_restr0.03861417
ELECTRON MICROSCOPYf_plane_restr0.0031546
ELECTRON MICROSCOPYf_dihedral_angle_d13.70293132

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