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- PDB-7pp1: Crystal structure of the P2Y12 receptor in complex with the inver... -

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Basic information

Entry
Database: PDB / ID: 7pp1
TitleCrystal structure of the P2Y12 receptor in complex with the inverse agonist selatogrel.
ComponentsP2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12
KeywordsMEMBRANE PROTEIN / Inverse agonist / complex
Function / homology
Function and homology information


visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration ...visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration / G protein-coupled adenosine receptor activity / hemostasis / cell projection membrane / regulation of chemotaxis / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / cell projection organization / positive regulation of ruffle assembly / positive regulation of cell adhesion mediated by integrin / lamellipodium assembly / cellular response to ATP / response to axon injury / monoatomic ion transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / establishment of localization in cell / calcium-mediated signaling / electron transport chain / platelet activation / ADP signalling through P2Y purinoceptor 12 / platelet aggregation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / cell surface / membrane / plasma membrane
Similarity search - Function
P2Y12 purinoceptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Selatogrel / CHOLESTEROL / Soluble cytochrome b562 / P2Y purinoceptor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsMac Sweeney, A. / Tidten-Luksch, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Pharmacol / Year: 2022
Title: Inverse agonist efficacy of selatogrel blunts constitutive P2Y12 receptor signaling by inducing the inactive receptor conformation.
Authors: Pons, V. / Garcia, C. / Tidten-Luksch, N. / Mac Sweeney, A. / Caroff, E. / Gales, C. / Riederer, M.A.
History
DepositionSep 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2543
Polymers53,2491
Non-polymers1,0052
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint1 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.090, 155.370, 47.310
Angle α, β, γ (deg.)90.000, 111.480, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12 / P2Y12 / ADP-glucose receptor / ADPG-R / P2T(AC) / P2Y(AC) / P2Y(cyc) / P2Y12 platelet ADP receptor ...P2Y12 / ADP-glucose receptor / ADPG-R / P2T(AC) / P2Y(AC) / P2Y(cyc) / P2Y12 platelet ADP receptor / P2Y(ADP) / SP1999 / Cytochrome b-562 / P2Y12 / ADP-glucose receptor / ADPG-R / P2T(AC) / P2Y(AC) / P2Y(cyc) / P2Y12 platelet ADP receptor / P2Y(ADP) / SP1999


Mass: 53248.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with ...Details: P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3,P2Y12 with thermostabilized BRIL in ICL3
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: P2RY12, HORK3, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H244, UniProt: P0ABE7
#2: Chemical ChemComp-7Y5 / Selatogrel / [(2~{R})-3-(4-butoxycarbonylpiperazin-1-yl)-2-[[6-[(3~{S})-3-methoxypyrrolidin-1-yl]-2-phenyl-pyrimidin-4-yl]carbonylamino]-3-oxidanylidene-propyl]phosphonic acid / [(2R)-3-(4-butoxycarbonylpiperazin-1-yl)-2-[[6-[(3S)-3-methoxypyrrolidin-1-yl]-2-phenyl-pyrimidin-4-yl]carbonylamino]-3-oxidanylidene-propyl]phosphonic acid / 4-((R)-2-((6-((S)-3-Methoxypyrrolidin-1-yl)-2-phenylpyrimidine-4-carbonyl)amino)-3-phosphonopropionyl)piperazine-1-carboxylic acid butyl ester


Mass: 618.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N6O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase
Details: 0.1 M ammonium formate, 0.1 M sodium cacdylate, pH 6.0-6.5, 25-35% PEG400
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→78.7 Å / Num. obs: 16554 / % possible obs: 98.9 % / Redundancy: 50.8 % / CC1/2: 0.99 / Net I/σ(I): 18.6
Reflection shellResolution: 2.78→2.87 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1494 / CC1/2: 0.5 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ntj

4ntj


Resolution: 2.78→45.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.218 / SU B: 20.968 / SU ML: 0.377 / Average fsc free: 0.7527 / Average fsc work: 0.769 / Cross valid method: FREE R-VALUE / ESU R: 0.674 / ESU R Free: 0.366 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2857 1630 9.945 %
Rwork0.2418 14760 -
all0.246 --
obs-16390 98.967 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 87.413 Å2
Baniso -1Baniso -2Baniso -3
1-4.695 Å2-0 Å20.05 Å2
2---6.221 Å20 Å2
3---1.135 Å2
Refinement stepCycle: LAST / Resolution: 2.78→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 71 1 2909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122975
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.6254055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36122.422128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.35515466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9781511
X-RAY DIFFRACTIONr_chiral_restr0.0860.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022161
X-RAY DIFFRACTIONr_nbd_refined0.2180.21567
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22089
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.279
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.218
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.22
X-RAY DIFFRACTIONr_mcbond_it4.3429.0681446
X-RAY DIFFRACTIONr_mcangle_it7.18713.5691797
X-RAY DIFFRACTIONr_scbond_it4.5069.1211527
X-RAY DIFFRACTIONr_scangle_it7.23613.6372258
X-RAY DIFFRACTIONr_lrange_it11.979122.1154717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.8520.5271050.513936X-RAY DIFFRACTION88.2952
2.852-2.930.3871130.3871083X-RAY DIFFRACTION99.8331
2.93-3.0150.3951180.3581041X-RAY DIFFRACTION99.3145
3.015-3.1080.3261140.352995X-RAY DIFFRACTION99.4619
3.108-3.2090.34970.305977X-RAY DIFFRACTION99.8141
3.209-3.3220.2751120.267943X-RAY DIFFRACTION100
3.322-3.4470.272970.213925X-RAY DIFFRACTION99.8047
3.447-3.5870.303960.228893X-RAY DIFFRACTION99.6976
3.587-3.7470.273990.24841X-RAY DIFFRACTION100
3.747-3.9290.266900.23821X-RAY DIFFRACTION100
3.929-4.1410.302800.23764X-RAY DIFFRACTION100
4.141-4.3910.349840.274737X-RAY DIFFRACTION100
4.391-4.6940.278750.234676X-RAY DIFFRACTION100
4.694-5.0680.265710.225642X-RAY DIFFRACTION100
5.068-5.550.335640.254588X-RAY DIFFRACTION99.8469
5.55-6.2010.376610.253539X-RAY DIFFRACTION100
6.201-7.1530.285530.229466X-RAY DIFFRACTION100
7.153-8.7420.195460.165398X-RAY DIFFRACTION100
8.742-12.2880.187350.133314X-RAY DIFFRACTION98.3099
12.288-45.680.19200.265180X-RAY DIFFRACTION98.5222

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