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- PDB-4ntj: Structure of the human P2Y12 receptor in complex with an antithro... -

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Basic information

Entry
Database: PDB / ID: 4ntj
TitleStructure of the human P2Y12 receptor in complex with an antithrombotic drug
ComponentsP2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12
KeywordsMEMBRANE PROTEIN / human P2Y12 receptor / GPCR network / lipidic cubic phase / antithrombotic drug / GPCR / PSI-Biology / Structural Genomics / Signaling Protein / membrane
Function / homology
Function and homology information


visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / regulation of microglial cell migration / G protein-coupled ADP receptor activity / cerebral cortex radial glia-guided migration / cell body membrane / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / positive regulation of microglial cell migration / positive regulation of monoatomic ion transport ...visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / regulation of microglial cell migration / G protein-coupled ADP receptor activity / cerebral cortex radial glia-guided migration / cell body membrane / P2Y receptors / G protein-coupled purinergic nucleotide receptor activity / positive regulation of microglial cell migration / positive regulation of monoatomic ion transport / hemostasis / G protein-coupled adenosine receptor activity / cell projection membrane / substrate-dependent cell migration, cell extension / regulation of chemotaxis / positive regulation of chemotaxis / cell projection organization / positive regulation of cell adhesion mediated by integrin / positive regulation of ruffle assembly / lamellipodium assembly / cellular response to ATP / response to axon injury / monoatomic ion transport / guanyl-nucleotide exchange factor activity / establishment of localization in cell / calcium-mediated signaling / electron transport chain / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / platelet activation / platelet aggregation / ADP signalling through P2Y purinoceptor 12 / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / iron ion binding / 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-AZJ / CHOLESTEROL / (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: 2.62 Å
AuthorsZhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. ...Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / 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: Structure of the human P2Y12 receptor in complex with an antithrombotic drug
Authors: Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / ...Authors: Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q.
History
DepositionDec 2, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name / _struct_ref_seq_dif.details
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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,P2Y purinoceptor 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2066
Polymers53,2491
Non-polymers1,9575
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.650, 156.430, 47.770
Angle α, β, γ (deg.)90.00, 111.08, 90.00
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


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: P2RY12, HORK3, cybC / Plasmid: pFASTBAC1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q9H244, UniProt: P0ABE7
#2: Chemical ChemComp-AZJ / ethyl 6-{4-[(benzylsulfonyl)carbamoyl]piperidin-1-yl}-5-cyano-2-methylpyridine-3-carboxylate


Mass: 470.541 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26N4O5S
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 15

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.91 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.05-0.15M ammonium formate, 0.1M sodium cacodylate, pH 6.0-6.5, 25-35% PEG 400, 200M AZD1283, Lipidic Cubic Phase, temperature 293K
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2013 / Details: mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19116 / % possible obs: 94.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 84.46 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1608 / % possible all: 79.5

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VW7 (PAR1), PDB ENTRY 1M6T (BRIL)

3vw7

1m6t


Resolution: 2.62→26.44 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE SOME UNKNOWN DENSITIES. LOCATED NEAR THE SIDE CHAIN OF TYR 32. THEY HAVE NOT BEEN MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 990 5.18 %RANDOM
Rwork0.2196 ---
obs0.2211 19094 94.18 %-
Displacement parametersBiso max: 225.79 Å2 / Biso mean: 106.1 Å2 / Biso min: 64.32 Å2
Baniso -1Baniso -2Baniso -3
1--14.0343 Å20 Å21.9204 Å2
2--14.1675 Å20 Å2
3----0.1332 Å2
Refine analyzeLuzzati coordinate error obs: 0.549 Å
Refinement stepCycle: LAST / Resolution: 2.62→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 127 12 3025
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013080HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054190HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1414SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes55HARMONIC2
X-RAY DIFFRACTIONt_gen_planes435HARMONIC5
X-RAY DIFFRACTIONt_it3080HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.16
X-RAY DIFFRACTIONt_other_torsion3.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion434SEMIHARMONIC5
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_contact3584SEMIHARMONIC4
LS refinement shellResolution: 2.62→2.76 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2567 107 4.5 %
Rwork0.232 2271 -
all0.233 2378 -
obs--94.18 %
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)
12.9964-1.6291-0.27785.32710.52771.9506-0.18180.0268-0.07740.1630.22220.5350.1073-0.0276-0.0405-0.12350.111-0.0508-0.32980.0404-0.179113.071987.536446.9005
26.3853-0.97881.54428.29641.50596.18190.04540.1219-0.3863-0.2775-0.22320.15580.2717-0.12920.1778-0.1463-0.04830.0222-0.2704-0.0579-0.201533.794848.448313.0903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|16 - A|312 }A16 - 312
2X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

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