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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 / cellular response to purine-containing compound / relaxation of muscle / G protein-coupled ADP receptor activity / A1 adenosine receptor binding / G protein-coupled purinergic nucleotide receptor signaling pathway / positive regulation of inositol trisphosphate biosynthetic process / P2Y receptors / positive regulation of penile erection / G protein-coupled purinergic nucleotide receptor activity ...G protein-coupled ATP receptor activity / cellular response to purine-containing compound / relaxation of muscle / G protein-coupled ADP receptor activity / A1 adenosine receptor binding / G protein-coupled purinergic nucleotide receptor signaling pathway / positive regulation of inositol trisphosphate biosynthetic process / P2Y receptors / positive regulation of penile erection / G protein-coupled purinergic nucleotide receptor activity / negative regulation of norepinephrine secretion / positive regulation of monoatomic ion transport / glial cell migration / signaling receptor regulator activity / regulation of presynaptic cytosolic calcium ion concentration / G protein-coupled adenosine receptor signaling pathway / response to growth factor / positive regulation of hormone secretion / signal transduction involved in regulation of gene expression / eating behavior / cellular response to ATP / regulation of synaptic vesicle exocytosis / response to mechanical stimulus / monoatomic ion transport / presynaptic active zone membrane / blood vessel diameter maintenance / protein localization to plasma membrane / establishment of localization in cell / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / ADP binding / platelet activation / 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-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor activity / regulation of cell shape / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / cell body / GTPase binding / Ca2+ pathway / fibroblast proliferation / scaffold protein binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / G alpha (q) signalling events / Ras protein signal transduction / postsynaptic membrane / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / cilium / apical plasma membrane / G protein-coupled receptor signaling pathway / protein heterodimerization activity / lysosomal membrane / GTPase activity / synapse / dendrite / protein-containing complex binding
Similarity search - Function
P2Y purinoceptor 1 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit ...P2Y purinoceptor 1 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / 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. / WD40 repeats / WD40 repeat / 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-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing 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)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
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

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_33503_half_map_2.map
Projections & Slices
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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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe selected images were 20eV using GIF-Quantum LS Imaging energy filter
Particle selectionNumber selected: 6184568
CTF correctionSoftware - Name: Gctf (ver. v1.06) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4nxw


Details: 6OIJ for G protein
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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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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