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- EMDB-37591: ADP-bound purinergic receptor 1 in complex with miniGs/q -

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Basic information

Entry
Database: EMDB / ID: EMD-37591
TitleADP-bound purinergic receptor 1 in complex with miniGs/q
Map data
Sample
  • Complex: ADP-bound purinergic receptor 1 in complex with miniGs/q
    • Protein or peptide: Soluble cytochrome b562,P2Y purinoceptor 1,Soluble cytochrome b562,P2Y purinoceptor 1
    • Protein or peptide: GNAS complex locus
    • Protein or peptide: Nanobody 35
    • 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CHOLESTEROL
KeywordsGPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / cellular response to purine-containing compound / A1 adenosine receptor binding / negative regulation of norepinephrine secretion / positive regulation of monoatomic ion transport ...G protein-coupled ATP receptor activity / relaxation of muscle / G protein-coupled ADP receptor activity / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / cellular response to purine-containing compound / A1 adenosine receptor binding / negative regulation of norepinephrine secretion / positive regulation of monoatomic ion transport / positive regulation of penile erection / 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 / regulation of synaptic vesicle exocytosis / cellular response to ATP / eating behavior / response to mechanical stimulus / monoatomic ion transport / 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 / electron transport chain / ADP binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / cilium / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / platelet activation / G-protein activation / 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 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / 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 / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / 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 / signaling receptor activity / regulation of cell shape / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cell body / G alpha (i) signalling events / scaffold protein binding / fibroblast proliferation / G alpha (s) signalling events / basolateral plasma membrane / G alpha (q) signalling events / postsynaptic membrane / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / periplasmic space / positive regulation of ERK1 and ERK2 cascade / electron transfer activity / postsynaptic density / cell surface receptor signaling pathway / iron ion binding / protein heterodimerization activity / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / apical plasma membrane / lysosomal membrane / GTPase activity / glutamatergic synapse
Similarity search - Function
P2Y purinoceptor 1 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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 ...P2Y purinoceptor 1 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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 / 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
Soluble cytochrome b562 / 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: 3.2 Å
AuthorsGu QC / Tang WQ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
Citation
Journal: To Be Published
Title: ADP-bound purinergic receptor 1 in complex with miniGs/q
Authors: Gu QC / Tang WQ
#1: Journal: To Be Published
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Gu QC / Tang WQ
History
DepositionSep 26, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_37591.png

Downloads & links

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Map

FileDownload / File: emd_37591.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.238
Minimum - Maximum-2.0627098 - 2.7249694
Average (Standard dev.)-0.0008533491 (±0.047552526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37591_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_37591_half_map_1.map
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Half map: #1

Fileemd_37591_half_map_2.map
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Sample components

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Entire : ADP-bound purinergic receptor 1 in complex with miniGs/q

EntireName: ADP-bound purinergic receptor 1 in complex with miniGs/q
Components
  • Complex: ADP-bound purinergic receptor 1 in complex with miniGs/q
    • Protein or peptide: Soluble cytochrome b562,P2Y purinoceptor 1,Soluble cytochrome b562,P2Y purinoceptor 1
    • Protein or peptide: GNAS complex locus
    • Protein or peptide: Nanobody 35
    • 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: CHOLESTEROL

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Supramolecule #1: ADP-bound purinergic receptor 1 in complex with miniGs/q

SupramoleculeName: ADP-bound purinergic receptor 1 in complex with miniGs/q
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5, #1, #4, #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: GNAS complex locus

MacromoleculeName: GNAS complex locus / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.840807 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGMGHHHHHH ENLYFQGNSK TEDQRNEEKA QREANKKIEK QLQKDKQVYR ATHRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNLFKSIWN NRWLRTISVI L FLNKQDLL ...String:
MGMGHHHHHH ENLYFQGNSK TEDQRNEEKA QREANKKIEK QLQKDKQVYR ATHRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNLFKSIWN NRWLRTISVI L FLNKQDLL AEKVLAGKSK IEDYFPEFAR YTTPEDATPE PGEDPRVTRA KYFIRDEFLR ISTASGDGRH YCYPHFTCAV DT ENARRIF NDCKDIILQM NLREYNLV

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.055867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWNGSSGG GGSGGGGSSG VSGWRLFKKI S

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

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Macromolecule #3: 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: 3 / 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 #4: Nanobody 35

MacromoleculeName: Nanobody 35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.057271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLEW VSDISQSGAS ISYTGSVKG RFTISRDNAK NTLYLQMNSL KPEDTAVYYC ARCPAPFTRD CFDVTSTTYA YRGQGTQVTV SSHHHHHH

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Macromolecule #5: Soluble cytochrome b562,P2Y purinoceptor 1,Soluble cytochrome b56...

MacromoleculeName: Soluble cytochrome b562,P2Y purinoceptor 1,Soluble cytochrome b562,P2Y purinoceptor 1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.586242 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLEFLEVL F QGPTEVLW ...String:
MKTIIALSYI FCLVFADYKD DDDAGRAHHH HHHHHHHENL YFQSGAPADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQK ATPPKLEDKS PDSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLEFLEVL F QGPTEVLW PAVPNGTDAA FLAGPGSSWG NSTVASTAAV SSSFKCALTK TGFQFYYLPA VYILVFIIGF LGNSVAIWMF VF HMKPWSG ISVYMFNLAL ADFLYVLTLP ALIFYYFNKT DWIFGDAMCK LQRFIFHVNL YGSILFLTCI SAHRYSGVVY PLK SLGRLK KKNAICISVL VWLIVVVAIS PILFYSGTGV RKNKTITCYD TTSDEYLRSY FIYSMCTTVA MFCVPLVLIL GCYG LIVRA LIYKDLDNSP LRRKSIYLVI IVLTVFAVSY IPFHVMKTMN LRARLDFQTP AMCAFNDRVY ATYQVTRGLA SLNSC VDPI LYFLAGDTFR RRLSRATRKA SRRSEANLQS KSEDMTLNVF TLEDFVGDWE QTAAYNLDQV LEQGGVSSLL QNLAVS VTP IQRIVRSGEN ALKIDIHVII PYEGLSADQM AQIEEVFKVV YPVDDHHFKV ILPYGTLVID GVTPNMLNYF GRPYEGI AV FDGKKITVTG TLWNGNKIID ERLITPDGSM LFRVTINS

UniProtKB: Soluble cytochrome b562, P2Y purinoceptor 1

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 376651
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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