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- PDB-4pxz: Crystal structure of P2Y12 receptor in complex with 2MeSADP -

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Basic information

Entry
Database: PDB / ID: 4pxz
TitleCrystal structure of P2Y12 receptor in complex with 2MeSADP
ComponentsP2Y purinoceptor 12, Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / purinergic receptor P2Y12 / agonist-bound / G-protein coupled receptor (GPCR) / signaling protein-agonist 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 / G protein-coupled purinergic nucleotide receptor activity / cell body membrane / : / positive regulation of monoatomic ion transport ...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 / G protein-coupled purinergic nucleotide receptor activity / cell body membrane / : / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration / G protein-coupled adenosine receptor activity / hemostasis / substrate-dependent cell migration, cell extension / cell projection membrane / positive regulation of chemotaxis / regulation of chemotaxis / cell projection organization / positive regulation of ruffle assembly / positive regulation of cell adhesion mediated by integrin / cellular response to ATP / lamellipodium assembly / response to axon injury / monoatomic ion transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / calcium-mediated signaling / establishment of localization in cell / ADP signalling through P2Y purinoceptor 12 / platelet aggregation / platelet activation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / electron transfer activity / periplasmic space / 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
Chem-6AD / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / P2Y purinoceptor 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 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)55,2857
Polymers53,2491
Non-polymers2,0366
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.110, 104.170, 169.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

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Protein , 1 types, 1 molecules A

#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: M1007W/H1102I/R1106L/D294N
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, P2Y12, cybC / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q9H244, UniProt: P0ABE7

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Non-polymers , 5 types, 55 molecules

#2: Chemical ChemComp-6AD / 2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) / 2-methylthio-adenosine-5'-diphosphate


Mass: 473.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N5O10P2S
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 17

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 30-40% PEG 400, 0.30-0.45M ammonium acetate, citrate, 3% v/v 1-Propanol, 0.1 M sodium citrate, pH 5.0, Lipidic cubic phase (LCP), temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONAPS 23-ID-D21.033
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDDec 8, 2013mirrors
MARMOSAIC 300 mm CCD2CCDNov 16, 2013mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Si double crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0331
ReflectionResolution: 2.5→50 Å / Num. obs: 20345 / % possible obs: 100 % / Redundancy: 16.5 % / Biso Wilson estimate: 60.18 Å2 / Rmerge(I) obs: 0.194 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VW7 and 1M6T

3vw7

1m6t


Resolution: 2.5→28.88 Å / Cor.coef. Fo:Fc: 0.9289 / Cor.coef. Fo:Fc free: 0.9196 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.333 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1041 5.12 %RANDOM
Rwork0.2005 ---
obs0.202 20345 100 %-
Displacement parametersBiso mean: 63.74 Å2
Baniso -1Baniso -2Baniso -3
1-5.5747 Å20 Å20 Å2
2---14.2671 Å20 Å2
3---8.6924 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 113 49 3295
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1555SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes63HARMONIC2
X-RAY DIFFRACTIONt_gen_planes465HARMONIC5
X-RAY DIFFRACTIONt_it3327HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion458SEMIHARMONIC5
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_contact3973SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3327HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4512HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion3.39
LS refinement shellResolution: 2.5→2.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2972 151 5.17 %
Rwork0.2242 2772 -
all0.2277 2923 -
obs--100 %
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)
11.431-0.1829-1.12050.38530.26283.0322-0.0170.4098-0.0245-0.131-0.142-0.0296-0.3077-0.55950.1590.14780.0349-0.02770.1848-0.00530.052119.098-2.32642.689
21.947-0.8568-1.95540.8450.83164.05560.0330.13740.03430.0158-0.05260.0957-0.292-0.58680.01960.13110.0393-0.02140.1069-0.03310.164949.247-17.708-1.365
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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