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- PDB-4py0: Crystal structure of P2Y12 receptor in complex with 2MeSATP -

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Basic information

Entry
Database: PDB / ID: 4py0
TitleCrystal structure of P2Y12 receptor in complex with 2MeSATP
ComponentsP2Y purinoceptor 12, Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / purinergic receptor P2Y12 / partial agonist-bound / G-protein coupled receptor (GPCR) / signaling protein-nucleotide complex / PSI-Biology / GPCR Network / Structural Genomics / signaling membrane protein / GPCR / platelet activation / membrane
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 / electron transport chain / calcium-mediated signaling / platelet activation / platelet aggregation / ADP signalling through P2Y purinoceptor 12 / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / periplasmic space / electron transfer activity / 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
Chem-6AT / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / P2Y purinoceptor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. ...Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2014
Title: Agonist-bound structure of the human P2Y12 receptor
Authors: Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / ...Authors: Zhang, J. / Zhang, K. / Gao, Z.G. / Paoletta, S. / Zhang, D. / Han, G.W. / Li, T. / Ma, L. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q.
History
DepositionMar 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Derived calculations
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,5154
Polymers53,2491
Non-polymers1,2663
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.650, 65.110, 100.740
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein P2Y purinoceptor 12, Soluble cytochrome b562 / 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


Mass: 53248.879 Da / Num. of mol.: 1 / Mutation: D294N, M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Details: Chimera protein of N-terminal residues 2-223 from P2Y12R (P2Y12_HUMAN), Soluble cytochrome b562 (C562_ECOLX), and C-terminal residues 224-342 from P2Y12R (P2Y12_HUMAN).
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HORK3, P2RY12, cybC / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q9H244, UniProt: P0ABE7
#2: Chemical ChemComp-6AT / 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate) / 2-methylthio-adenosine-5'-triphosphate


Mass: 553.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3S
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 35-40% PEG 400, 0.15-0.20M ammonium tartrate, 4% v/v MPD, 0.1M sodium citrate, pH 6.0, Lipidic cubic phase (LCP), temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2013 / Details: mirrors
RadiationMonochromator: Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 8273 / % possible obs: 92.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 87.79 Å2 / Rmerge(I) obs: 0.222 / Net I/σ(I): 5.6
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.2 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PXZ and 1M6T

4pxz

1m6t


Resolution: 3.1→28.81 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.8638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.498
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 422 5.1 %RANDOM
Rwork0.2216 ---
obs0.2239 8273 92.33 %-
Displacement parametersBiso mean: 88.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.8922 Å20 Å20.6083 Å2
2---0.3371 Å20 Å2
3----2.5552 Å2
Refine analyzeLuzzati coordinate error obs: 0.653 Å
Refinement stepCycle: LAST / Resolution: 3.1→28.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 65 1 3112
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1448SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes56HARMONIC2
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it3190HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3707SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3190HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4341HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion1.68
X-RAY DIFFRACTIONt_other_torsion3.24
LS refinement shellResolution: 3.1→3.47 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2876 115 5.02 %
Rwork0.2248 2178 -
all0.2277 2293 -
obs--92.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56170.21370.33020.9639-0.28730.0491-0.1393-0.50870.20830.534-0.1158-0.3719-0.1519-0.2820.25510.70490.0947-0.16880.279-0.04030.3761-13.485-10.127-0.115
20.86980.44981.6071.51120.92827.1701-0.0584-0.01240.15090.4882-0.2147-0.2456-0.3026-0.39630.2731-0.02810.05430.14810.0338-0.04460.184817.502-25.972-43.415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|15 - A|305 }A15 - 305
2X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

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