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- PDB-4xnw: The human P2Y1 receptor in complex with MRS2500 -

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Basic information

Entry
Database: PDB / ID: 4xnw
TitleThe human P2Y1 receptor in complex with MRS2500
ComponentsP2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
KeywordsTRANSPORT PROTEIN / human P2Y1 receptor / G protein coupled receptor / platelet activation / membrane protein / 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 / positive regulation of inositol trisphosphate biosynthetic process / G protein-coupled purinergic nucleotide receptor activity / 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 / positive regulation of inositol trisphosphate biosynthetic process / G protein-coupled purinergic nucleotide receptor activity / 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 / signal transduction involved in regulation of gene expression / positive regulation of hormone secretion / response to growth factor / cellular response to ATP / regulation of synaptic vesicle exocytosis / eating behavior / monoatomic ion transport / response to mechanical stimulus / presynaptic active zone membrane / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / blood vessel diameter maintenance / establishment of localization in cell / ADP binding / protein localization to plasma membrane / cilium / platelet activation / ADP signalling through P2Y purinoceptor 1 / signaling receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / cell body / positive regulation of cytosolic calcium ion concentration / regulation of cell shape / postsynaptic membrane / scaffold protein binding / G alpha (q) signalling events / basolateral plasma membrane / postsynaptic density / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / apical plasma membrane / iron ion binding / positive regulation of protein phosphorylation / protein heterodimerization activity / dendrite / glutamatergic synapse / 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-2ID / Rubredoxin / P2Y purinoceptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 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
C: P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1906
Polymers94,9372
Non-polymers1,2534
Water18010
1
A: P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0953
Polymers47,4681
Non-polymers6272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: P2Y purinoceptor 1,Rubredoxin,P2Y purinoceptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0953
Polymers47,4681
Non-polymers6272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.670, 64.970, 77.570
Angle α, β, γ (deg.)101.82, 95.70, 100.85
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A38 - 333
2010C38 - 333
1020A1001 - 1054
2020C1001 - 1054

NCS ensembles :
ID
1
2

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Components

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


Mass: 47468.289 Da / Num. of mol.: 2 / 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
#2: Chemical ChemComp-2ID / [(1R,2S,4S,5S)-4-[2-iodo-6-(methylamino)-9H-purin-9-yl]-2-(phosphonooxy)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate


Mass: 561.163 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H18IN5O8P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG400 Sodium citrate HEPES

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 20471 / % possible obs: 98.2 % / Redundancy: 4.9 % / Net I/σ(I): 18.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.7→29.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 8.27 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26714 1027 5.1 %RANDOM
Rwork0.21834 ---
obs0.22094 19283 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.213 Å2
Baniso -1Baniso -2Baniso -3
1-13.03 Å24.64 Å20.66 Å2
2--8.83 Å2-3.55 Å2
3----21.86 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 60 10 5639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025794
X-RAY DIFFRACTIONr_bond_other_d0.0040.025520
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9737902
X-RAY DIFFRACTIONr_angle_other_deg0.9873.00312641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36222.345226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58715928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5331527
X-RAY DIFFRACTIONr_chiral_restr0.0760.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216342
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021395
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A16976
12C16976
21A2684
22C2684
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 71 -
Rwork0.303 1370 -
obs--97.36 %

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