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- PDB-4xnv: The human P2Y1 receptor in complex with BPTU -

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Basic information

Entry
Database: PDB / ID: 4xnv
TitleThe human P2Y1 receptor in complex with BPTU
ComponentsP2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1
KeywordsTRANSPORT PROTEIN/INHIBITOR / human P2Y1 receptor / G protein coupled receptor / platelet activation / membrane protein / inhibitor complex / TRANSPORT PROTEIN-INHIBITOR complex / PSI-Biology / Structural Genomics / GPCR Network / GPCR
Function / homology
Function and homology information


G protein-coupled ATP receptor activity / relaxation of muscle / A1 adenosine receptor binding / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection ...G protein-coupled ATP receptor activity / relaxation of muscle / A1 adenosine receptor binding / G protein-coupled ADP receptor activity / P2Y receptors / cellular response to purine-containing compound / G protein-coupled purinergic nucleotide receptor activity / positive regulation of inositol trisphosphate biosynthetic process / positive regulation of monoatomic ion transport / positive regulation of penile erection / negative regulation of norepinephrine secretion / glial cell migration / regulation of presynaptic cytosolic calcium ion concentration / G protein-coupled adenosine receptor signaling pathway / positive regulation of hormone secretion / signal transduction involved in regulation of gene expression / response to growth factor / cellular response to ATP / regulation of synaptic vesicle exocytosis / eating behavior / monoatomic ion transport / presynaptic active zone membrane / response to mechanical stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / blood vessel diameter maintenance / protein localization to plasma membrane / establishment of localization in cell / ADP binding / cilium / platelet activation / ADP signalling through P2Y purinoceptor 1 / signaling receptor activity / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / G alpha (q) signalling events / postsynaptic membrane / basolateral plasma membrane / postsynaptic density / electron transfer activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / iron ion binding / apical plasma membrane / G protein-coupled receptor signaling pathway / protein heterodimerization activity / glutamatergic synapse / dendrite / cell surface / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane
Similarity search - Function
P2Y purinoceptor 1 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...P2Y purinoceptor 1 / Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / 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)
Similarity search - Domain/homology
Chem-BUR / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / CHOLESTEROL HEMISUCCINATE / Rubredoxin / P2Y purinoceptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsZhang, D. / Gao, Z. / Jacobson, K. / Han, G.W. / Stevens, R. / Zhao, Q. / Wu, B. / GPCR Network (GPCR)
CitationJournal: Nature / Year: 2015
Title: Two disparate ligand-binding sites in the human P2Y1 receptor
Authors: Zhang, D. / Gao, Z.G. / Zhang, K. / Kiselev, E. / Crane, S. / Wang, J. / Paoletta, S. / Yi, C. / Ma, L. / Zhang, W. / Han, G.W. / Liu, H. / Cherezov, V. / Katritch, V. / Jiang, H. / Stevens, ...Authors: Zhang, D. / Gao, Z.G. / Zhang, K. / Kiselev, E. / Crane, S. / Wang, J. / Paoletta, S. / Yi, C. / Ma, L. / Zhang, W. / Han, G.W. / Liu, H. / Cherezov, V. / Katritch, V. / Jiang, H. / Stevens, R.C. / Jacobson, K.A. / Zhao, Q. / Wu, B.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,91716
Polymers47,4681
Non-polymers5,44815
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-1 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 66.270, 239.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein P2Y purinoceptor 1, Rubredoxin, P2Y purinoceptor 1 / P2Y1 / ATP receptor / Purinergic receptor


Mass: 47468.289 Da / Num. of mol.: 1 / Mutation: D320N
Source method: isolated from a genetically manipulated source
Details: Chimera protein of P2Y purinoceptor 1 (P2RY1_HUMA) with Rubredoxin (RUBR_CLOPA) inserted into ICL3 domain between residues 247LYS and 253PRO, and replaced residues 248ASN to 252SER.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria)
Gene: P2RY1 / Production host: Spodoptera (butterflies/moths) / References: UniProt: P47900, UniProt: P00268

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Non-polymers , 7 types, 45 molecules

#2: Chemical ChemComp-BUR / 1-[2-(2-tert-butylphenoxy)pyridin-3-yl]-3-[4-(trifluoromethoxy)phenyl]urea


Mass: 445.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22F3N3O3
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H50O4
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG2000MME Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 19881 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.95 Å2 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.2→41.4 Å / Cor.coef. Fo:Fc: 0.9412 / Cor.coef. Fo:Fc free: 0.9312 / SU R Cruickshank DPI: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.265 / SU Rfree Blow DPI: 0.19 / SU Rfree Cruickshank DPI: 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 1017 5.12 %RANDOM
Rwork0.2066 ---
obs0.2078 19881 99.94 %-
Displacement parametersBiso mean: 63.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.5204 Å20 Å20 Å2
2---2.5204 Å20 Å2
3---5.0409 Å2
Refine analyzeLuzzati coordinate error obs: 0.369 Å
Refinement stepCycle: LAST / Resolution: 2.2→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 371 30 3114
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013164HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.044262HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1126SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes440HARMONIC5
X-RAY DIFFRACTIONt_it3164HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.19
X-RAY DIFFRACTIONt_other_torsion17.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion406SEMIHARMONIC5
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_contact3716SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3786 133 4.61 %
Rwork0.3661 2754 -
all0.3667 2887 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -11.1074 Å / Origin y: 17.9445 Å / Origin z: 9.7233 Å
111213212223313233
T-0.1738 Å20.0229 Å20.0008 Å2--0.1537 Å2-0.0413 Å2---0.0538 Å2
L1.7026 °20.0833 °20.3764 °2-2.2469 °20.055 °2--1.0152 °2
S0.0034 Å °-0.2893 Å °0.2711 Å °0.2173 Å °0.021 Å °0.2022 Å °-0.0437 Å °-0.0951 Å °-0.0244 Å °
Refinement TLS groupSelection details: { A|39 - A|334 }

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