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- PDB-5uig: Crystal structure of adenosine A2A receptor bound to a novel tria... -

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Basic information

Entry
Database: PDB / ID: 5uig
TitleCrystal structure of adenosine A2A receptor bound to a novel triazole-carboximidamide antagonist
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsADENOSINE BINDING PROTEIN / Adenosine / A2A receptor / GPCR / vapor diffusion / allosteric / Parkinson's disease
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / astrocyte activation / presynaptic modulation of chemical synaptic transmission / response to amphetamine / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / heme binding / dendrite / lipid binding / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / 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-8D1 / Chem-EDT / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSun, B. / Bachhawat, P. / Ling-Hon Chu, M. / Ceska, T. / Sands, Z. / Lebon, F. / Kobilka, T.S. / Kobilka, B.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket.
Authors: Sun, B. / Bachhawat, P. / Chu, M.L. / Wood, M. / Ceska, T. / Sands, Z.A. / Mercier, J. / Lebon, F. / Kobilka, T.S. / Kobilka, B.K.
History
DepositionJan 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Mar 8, 2017Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3654
Polymers49,5411
Non-polymers8243
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint5 kcal/mol
Surface area18880 Å2
2
A: Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules

A: Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7308
Polymers99,0822
Non-polymers1,6486
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area4690 Å2
ΔGint-23 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.222, 131.222, 89.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a / Cytochrome b-562


Mass: 49540.879 Da / Num. of mol.: 1
Mutation: M1007W, H1102I, R1106L,M1007W, H1102I, R1106L,M1007W, H1102I, R1106L
Source method: isolated from a genetically manipulated source
Details: The protein is a chimera with BRIL inserted between L208 and E219
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7
#2: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-8D1 / 5-amino-N-[(2-methoxyphenyl)methyl]-2-(3-methylphenyl)-2H-1,2,3-triazole-4-carboximidamide


Mass: 336.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N6O
Has protein modificationY

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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: 3.9 Å3/Da / Density % sol: 68.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.045 M MES, 0.045 M MgCl2, 28% PEG400, 5% Jeffamine M-600 (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→131.22 Å / Num. obs: 18101 / % possible obs: 95.5 % / Redundancy: 6.3 % / CC1/2: 0.984 / Net I/σ(I): 11

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 3.5→131.22 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / ESU R Free: 0.59 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29883 509 5 %RANDOM
Rwork0.27603 ---
obs0.27719 9658 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.781 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--1.56 Å20 Å2
3----3.12 Å2
Refinement stepCycle: 1 / Resolution: 3.5→131.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2848 0 57 0 2905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.9624107
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6875388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64724.074108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71515415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.752159
X-RAY DIFFRACTIONr_chiral_restr0.0520.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212247
X-RAY DIFFRACTIONr_gen_planes_other
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_it5.8868.9431558
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.92813.3951944
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7438.9991442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.65975.6364882
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 33 -
Rwork0.334 615 -
obs--85.6 %

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