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- EMDB-33503: Cryo-EM structure of the purinergic receptor P2Y1R in complex wit... -

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Entry
Database: EMDB / ID: EMD-33503
TitleCryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11
Map data
Sample
  • Complex: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16
    • Protein or peptide: Guanine nucleotide-binding protein G(11) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: scfv16
  • Protein or peptide: P2Y purinoceptor 1
  • Ligand: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)
KeywordsG protein-coupled receptor / purinergic receptor / P2Y1R / ligand binding / signal transduction / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled ATP receptor activity / relaxation of muscle / A1 adenosine receptor binding / 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 ...G protein-coupled ATP receptor activity / relaxation of muscle / A1 adenosine receptor binding / 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 / glial cell migration / regulation of presynaptic cytosolic calcium ion concentration / G protein-coupled adenosine receptor signaling pathway / signal transduction involved in regulation of gene expression / positive regulation of hormone secretion / response to growth factor / cellular response to ATP / regulation of synaptic vesicle exocytosis / eating behavior / monoatomic ion transport / response to mechanical stimulus / presynaptic active zone membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / blood vessel diameter maintenance / establishment of localization in cell / protein localization to plasma membrane / ADP binding / 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 / cilium / 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 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / platelet activation / 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 / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / 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) / retina development in camera-type eye / signaling receptor activity / GTPase binding / Ca2+ pathway / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell shape / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / G alpha (s) signalling events / scaffold protein binding / G alpha (q) signalling events / postsynaptic membrane / basolateral plasma membrane / Ras protein signal transduction / cell population proliferation / 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 / dendrite / synapse / glutamatergic synapse / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTan Q / Li B / Han S / Zhao Q / Wu B
Funding support China, 5 items
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, 2022-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33503.png

Downloads & links

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Map

FileDownload / File: emd_33503.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.045 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.16960609 - 0.2167304
Average (Standard dev.)0.0000242759 (±0.0050432347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33503_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33503_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16

EntireName: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16
Components
  • Complex: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16
    • Protein or peptide: Guanine nucleotide-binding protein G(11) subunit alpha
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: scfv16
  • Protein or peptide: P2Y purinoceptor 1
  • Ligand: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)

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Supramolecule #1: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16

SupramoleculeName: The purinergic receptor P2Y1R in complex with 2MeSADP, G11 and scfv16
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#5 / Details: scf16 was recombinantly expressed in sf9 cells
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10 kDa/nm

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Macromolecule #1: P2Y purinoceptor 1

MacromoleculeName: P2Y purinoceptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.296887 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GAPTEVLWPA VPNGTDAAFL AGPGSSWGNS TVASTAAVSS SFKCALTKTG FQFYYLPAVY ILVFIIGFLG NSVAIWMFVF HMKPWSGIS VYMFNLALAD FLYVLTLPAL IFYYFNKTDW IFGDAMCKLQ RFIFHVNLYG SILFLTCISA HRYSGVVYPL K SLGRLKKK ...String:
GAPTEVLWPA VPNGTDAAFL AGPGSSWGNS TVASTAAVSS SFKCALTKTG FQFYYLPAVY ILVFIIGFLG NSVAIWMFVF HMKPWSGIS VYMFNLALAD FLYVLTLPAL IFYYFNKTDW IFGDAMCKLQ RFIFHVNLYG SILFLTCISA HRYSGVVYPL K SLGRLKKK NAICISVLVW LIVVVAISPI LFYSGTGVRK NKTITCYDTT SDEYLRSYFI YSMCTTVAMF CVPLVLILGC YG LIVRALI YKDLDNSPLR RKSIYLVIIV LTVFAVSYIP FHVMKTMNLR ARLDFQTPAM CAFNDRVYAT YQVTRGLASL NSC VDPILY FLAGDTFRRR LSRATRKASR RSEANLQSKS EDMTLNILPE FKQNGDTSLE FLEVLFQGPG SWSHPQFEKG SGAG ASAGS WSHPQFEK

UniProtKB: P2Y purinoceptor 1

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

MacromoleculeName: Guanine nucleotide-binding protein G(11) subunit alpha
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.385281 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLRRDKRDA RRELKLLLLG TGESGKSTFI KQMRIIHGAG YSEEDKRGFT KLVYQNIFTA MQAMIRAME TLKILYKYEQ NKANALLIRE VDVEKVTTFE HQYVSAIKTL WEDPGIQECY DRRREYQLSD SAKYYLTDVD R IATLGYLP ...String:
MGCTLSAEDK AAVERSKMID RNLRRDKRDA RRELKLLLLG TGESGKSTFI KQMRIIHGAG YSEEDKRGFT KLVYQNIFTA MQAMIRAME TLKILYKYEQ NKANALLIRE VDVEKVTTFE HQYVSAIKTL WEDPGIQECY DRRREYQLSD SAKYYLTDVD R IATLGYLP TQQDVLRVRV PTTGIIEYPF DLENIIFRMV DVGGQRSERR KWIHCFENVT SIMFLVALSE YDQVLVESDN EN RMEESKA LFRTIITYPW FQNSSVILFL NKKDLLEDKI LYSHLVDYFP EFDGPQRDAQ AAREFILKMF VDLNPDSDKI IYS HFTCAT DTENIRFVFA AVKDTILQLN LKEYNLV

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.245805 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG ...String:
MHHHHHHSEL DQLRQEAEQL KNQIRDARKA CADATLSQIT NNIDPVGRIQ MRTRRTLRGH LAKIYAMHWG TDSRLLVSAS QDGKLIIWD SYTTNKVHAI PLRSSWVMTC AYAPSGNYVA CGGLDNICSI YNLKTREGNV RVSRELAGHT GYLSCCRFLD D NQIVTSSG DTTCALWDIE TGQQTTTFTG HTGDVMSLSL APDTRLFVSG ACDASAKLWD VREGMCRQTF TGHESDINAI CF FPNGNAF ATGSDDATCR LFDLRADQEL MTYSHDNIIC GITSVSFSKS GRLLLAGYDD FNCNVWDALK ADRAGVLAGH DNR VSCLGV TDDGMAVATG SWDSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #5: scfv16

MacromoleculeName: scfv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.337307 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL

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Macromolecule #6: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)

MacromoleculeName: 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)
type: ligand / ID: 6 / Number of copies: 1 / Formula: 6AD
Molecular weightTheoretical: 473.293 Da
Chemical component information

ChemComp-6AD:
2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)

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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

Concentration2.0 mg/mL
BufferpH: 7.5 / Component - Concentration: 2.0 mg/ml / Component - Formula: 150mM / Component - Name: sodium chloride
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 1s.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 9856 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2 / Details: Images were collected in movie-mode
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6184568
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4nxw


Details: 6OIJ for G protein
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 659399
DetailsThe selected images were 20eV using GIF-Quantum LS Imaging energy filter

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Atomic model buiding 1

Initial modelPDB ID:

4nxw


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Overall B value: 43.86
Output model

PDB-7xxh:
Cryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11

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