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- PDB-8rln: Crystal structure of human adenosine A2A receptor (construct A2A-... -

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Basic information

Entry
Database: PDB / ID: 8rln
TitleCrystal structure of human adenosine A2A receptor (construct A2A-PSB2-bRIL) complexed with the partial antagonist LUF5834 at the orthosteric pocket
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / BRIL / ANTAGONIST / PURINERGIC SIGNALING / CANCER IMMUNOTHERAPY
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / vasodilation / 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 / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / heme binding / dendrite / 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
: / CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.43 Å
AuthorsStrater, N. / Claff, T. / Weisse, R.H. / Muller, C.E.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 1873 Germany
German Research Foundation (DFG)GRK 2873 Germany
German Research Foundation (DFG)SFB 1328 Germany
German Research Foundation (DFG)SFB 1423, project number 421152132, subproject A6 Germany
German Federal Ministry for Education and ResearchBonn Graduate School of Drug Sciences (BIGS-DrugS) Germany
CitationJournal: Acs Pharmacol Transl Sci / Year: 2024
Title: Structural Insights into Partial Activation of the Prototypic G Protein-Coupled Adenosine A 2A Receptor.
Authors: Claff, T. / Mahardhika, A.B. / Vaassen, V.J. / Schlegel, J.G. / Vielmuth, C. / Weisse, R.H. / Strater, N. / Muller, C.E.
History
DepositionJan 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,32814
Polymers48,1571
Non-polymers4,17013
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint19 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.556, 179.693, 140.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48157.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 57 molecules

#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#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-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-A1H1S / 2-azanyl-4-(4-hydroxyphenyl)-6-(1~{H}-imidazol-2-ylmethylsulfanyl)pyridine-3,5-dicarbonitrile


Mass: 348.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H12N6OS / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.2
Details: 23% (w/v) PEG400, 90 mM sodium thiocyanate, 100 mM sodium citrate pH 5.2, and 2% (w/v) 2,5 hexandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97621 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97621 Å / Relative weight: 1
ReflectionResolution: 2.43→89.85 Å / Num. obs: 16837 / % possible obs: 86.4 % / Redundancy: 12.1 % / Biso Wilson estimate: 43.05 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.076 / Rrim(I) all: 0.264 / Net I/σ(I): 7.9
Reflection shellResolution: 2.43→2.59 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 843 / CC1/2: 0.493 / Rpim(I) all: 0.609 / Rrim(I) all: 2.201 / % possible all: 25

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
autoPROCdata processing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.43→70.23 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 866 5.15 %
Rwork0.2029 --
obs0.2069 16825 86.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→70.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 251 44 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133378
X-RAY DIFFRACTIONf_angle_d1.4224574
X-RAY DIFFRACTIONf_dihedral_angle_d15.5191308
X-RAY DIFFRACTIONf_chiral_restr0.055532
X-RAY DIFFRACTIONf_plane_restr0.009575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.580.3715350.2301646X-RAY DIFFRACTION22
2.58-2.780.39841670.2472876X-RAY DIFFRACTION95
2.78-3.060.34031420.23643073X-RAY DIFFRACTION100
3.06-3.50.34091820.23123031X-RAY DIFFRACTION100
3.5-4.410.24661860.17313086X-RAY DIFFRACTION100
4.41-70.230.23361540.19053247X-RAY DIFFRACTION100

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