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- PDB-8gne: Crystal structure of human adenosine A2A receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 8gne
TitleCrystal structure of human adenosine A2A receptor in complex with an insurmountable inverse agonist, KW-6356.
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN/INHIBITOR / adenosine A2A receptor / inverse agonist / insurmountable antagonism / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / synaptic transmission, cholinergic / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / electron transport chain / positive regulation of apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / periplasmic space / electron transfer activity / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / 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 / Chem-JQR / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuzuki, M. / Saito, J. / Miyagi, H. / Yasunaga, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Pharmacol. / Year: 2023
Title: In Vitro Pharmacological Profile of KW-6356, a Novel Adenosine A 2A Receptor Antagonist/Inverse Agonist.
Authors: Ohno, Y. / Suzuki, M. / Asada, H. / Kanda, T. / Saki, M. / Miyagi, H. / Yasunaga, M. / Suno, C. / Iwata, S. / Saito, J.I. / Uchida, S.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,52525
Polymers48,1721
Non-polymers8,35324
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.350, 180.510, 141.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 48172.016 Da / Num. of mol.: 1 / Mutation: N154Q,M1007W,H1102I,R1106L
Source method: isolated from a genetically manipulated source
Details: -1-208 Adenosine receptor A2a;1001-1106 Soluble cytochrome b562;219-309 Adenosine receptor A2a
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

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Non-polymers , 6 types, 87 molecules

#2: Chemical ChemComp-JQR / ~{N}-[4-(furan-2-yl)-5-(oxan-4-ylcarbonyl)-1,3-thiazol-2-yl]-6-methyl-pyridine-3-carboxamide


Mass: 397.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / 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.: 18 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 5
Details: PEG 400, sodium thiocyanate, 2,5-hexanediol, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.08 Å / Num. obs: 22863 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.066 / Rrim(I) all: 0.184 / Net I/σ(I): 6.9 / Num. measured all: 161217 / Scaling rejects: 131
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.384.31.14909821200.4020.5671.2841.197.4
8.91-47.087.20.06333454660.9860.0270.06916.199.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0232refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EYI

4eyi


Resolution: 2.3→45.17 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 16.507 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2346 1119 4.9 %RANDOM
Rwork0.1904 ---
obs0.1927 21714 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.2 Å2 / Biso mean: 50.332 Å2 / Biso min: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---1.74 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 2.3→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3010 0 496 63 3569
Biso mean--70.27 45.07 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133584
X-RAY DIFFRACTIONr_bond_other_d0.0080.0173648
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.7354787
X-RAY DIFFRACTIONr_angle_other_deg1.2991.7778467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52321.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93515499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2791515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 70 -
Rwork0.33 1511 -
all-1581 -
obs--96.23 %
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)
10.79754.24230.286922.79781.49960.1070.1147-0.05080.01240.6851-0.0930.2940.0458-0.0466-0.02170.378-0.01360.00950.42880.01350.34825.1151-20.65792.0383
21.11632.11130.833915.70084.9042.3892-0.03320.06660.0206-0.24840.1019-0.2873-0.02490.1404-0.06870.106-0.00130.02950.230.01740.031711.4465.60587.0267
32.9302-3.10161.67678.18950.77642.2975-0.3988-0.27840.5199-0.45270.191-0.6238-0.7148-0.18470.20780.3731-0.07030.08380.2085-0.0820.26089.200828.412116.5819
41.6625-2.2917-0.532613.22642.8171.70360.0920.00980.048-0.1153-0.06980.0651-0.10540.1798-0.02220.0748-0.02520.00080.1992-0.00160.00469.81636.194816.4861
54.95517.48155.538611.82538.60456.30320.4543-0.2189-0.2650.4452-0.2882-0.12670.4135-0.2206-0.16610.27890.0269-0.07210.28680.06390.210213.2641-14.48923.2639
63.7675-6.5026-0.392813.4057-0.17081.0846-0.0662-0.01350.01370.16020.06220.1263-0.04630.04110.0040.0854-0.0239-0.01870.1953-0.01180.02512.193210.093923.7427
79.843-7.85047.001512.6225-0.20879.5372-0.7583-0.97040.40520.82550.20250.0244-0.3655-1.08930.55580.3742-0.05430.08920.5066-0.0720.1624-2.725732.027129.0227
81.22580.18890.30339.9930.93320.2944-0.144-0.08180.16140.49160.1796-0.1759-0.09780.0917-0.03570.1844-0.00920.00510.2266-0.02150.06427.789112.657930.2947
95.3647-7.3338-2.813312.46793.23533.0916-0.0557-0.018-0.7878-0.2084-0.12720.25760.62410.28040.18290.2390.0381-0.05470.2906-0.01640.5176.2667-16.222425.6385
100.4584-1.54730.681210.4082-2.69121.1476-0.0913-0.02350.00530.12080.21730.2806-0.1596-0.076-0.1260.12330.0260.03130.2027-0.00180.1442-9.09529.256524.7876
117.922-8.743-1.90549.71712.15270.64890.09350.5423-0.1883-0.1037-0.49650.4761-0.3103-0.23460.4030.55390.174-0.30590.46160.08331.2199-23.041144.586717.5384
125.9098-2.56013.34715.9183-0.49627.9531-0.06740.1127-0.47160.3948-0.21460.5964-0.1109-0.330.2820.40510.00290.11350.50740.09840.9527-24.37553.608925.9625
1314.5449-5.1754-5.47169.90162.57218.1077-0.2247-0.8171-0.2438-0.39930.5275-0.07350.01430.4612-0.30290.3866-0.0204-0.06040.43960.00830.6001-16.119558.828523.7769
141.4829-3.9578-0.50511.0441.42470.19970.2533-0.03920.3255-0.9667-0.1542-0.4074-0.1945-0.0784-0.09920.62940.1347-0.02850.5273-0.02850.6912-16.970852.30415.0129
151.1949-3.44460.196214.3833-0.47690.0644-0.14210.06950.0846-0.01670.15220.3159-0.0907-0.0106-0.01010.1720.00810.00690.22930.00890.1494-5.5616.024313.6687
169.05067.5905-6.08696.9414-4.34875.32010.02550.48070.57580.17730.37120.60370.1991-0.3471-0.39670.0419-0.00350.01940.1587-00.1784-8.6589-5.597618.8804
1710.72994.7368-1.50165.0747-4.23334.5676-0.82570.2177-1.2647-0.92660.4048-0.61630.8159-0.47790.42090.3088-0.07440.13010.1921-0.19950.485-8.1063-14.478613.2652
182.58195.1941-0.434516.25081.44192.2081-0.11890.05450.0058-0.20160.16390.19620.1752-0.0203-0.0450.08210.00470.00310.2282-0.02060.07120.5131-1.69899.5872
191.8974-4.4275-1.123411.75352.1183.29850.18010.0793-0.0389-0.4261-0.0390.0856-0.1448-0.3588-0.14110.1801-0.00860.01020.2054-0.00310.09231.192717.89257.2241
207.4521-1.2076-1.40963.60162.08713.4450.15960.61720.4523-0.2765-0.0665-0.4054-0.01210.1174-0.09310.26720.0131-0.00150.25680.00950.199511.668124.65412.3537
2114.8401-1.6587-7.06519.845-6.83929.3895-0.71790.0092-0.3928-0.28760.3837-0.14220.6191-0.3080.33420.256-0.01650.01440.24760.03620.02470.6559-7.032718.0251
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 2
2X-RAY DIFFRACTION2A3 - 32
3X-RAY DIFFRACTION3A33 - 40
4X-RAY DIFFRACTION4A41 - 68
5X-RAY DIFFRACTION5A69 - 75
6X-RAY DIFFRACTION6A76 - 106
7X-RAY DIFFRACTION7A107 - 117
8X-RAY DIFFRACTION8A118 - 138
9X-RAY DIFFRACTION9A139 - 174
10X-RAY DIFFRACTION10A175 - 203
11X-RAY DIFFRACTION11A204 - 208
12X-RAY DIFFRACTION11A1001 - 1020
13X-RAY DIFFRACTION12A1022 - 1042
14X-RAY DIFFRACTION13A1058 - 1082
15X-RAY DIFFRACTION14A1083 - 1106
16X-RAY DIFFRACTION14A219 - 227
17X-RAY DIFFRACTION15A228 - 246
18X-RAY DIFFRACTION16A247 - 258
19X-RAY DIFFRACTION17A259 - 268
20X-RAY DIFFRACTION18A269 - 282
21X-RAY DIFFRACTION19A283 - 292
22X-RAY DIFFRACTION20A293 - 309
23X-RAY DIFFRACTION21A1201

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