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- PDB-5mzj: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5mzj
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with theophylline at 2.0A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-PROTEIN-COUPLED RECEPTOR / INTEGRAL THERMOSTABILIZING MUTATIONS
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 / positive regulation of protein secretion / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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
CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THEOPHYLLINE / 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 Å
AuthorsCheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
CitationJournal: Structure / Year: 2017
Title: Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity.
Authors: Cheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 23, 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)58,14135
Polymers48,0681
Non-polymers10,07334
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint48 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.246, 179.867, 139.398
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,Adenosine receptor A2a / Cytochrome b-562


Mass: 48067.824 Da / Num. of mol.: 1
Mutation: A54L, T88A, R107A, K122A, N154A, L202A,M1007W,L235A, V239A, S277A, G318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Plasmid: PFAST-BAC / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): TNI PRO / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 195 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-TEP / THEOPHYLLINE


Mass: 180.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N4O2
#4: Chemical ChemComp-CLR / CHOLESTEROL


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


Mass: 282.461 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1M MES PH 5.5, 0.2M K/NA TARTRATE, 27.5-40% PEG400, 0.5-1% (V/V) (+/-)-2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2016 / Details: (DOUBLE) KB MIRROR PAIR
RadiationMonochromator: DOUBLE SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96857 Å / Relative weight: 1
ReflectionResolution: 2→33.6 Å / Num. obs: 64345 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 9.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2467 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
XDSv1.0data reduction
Aimlessv0.5.17data scaling
PHASERphasing
PHENIXv1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 2→33.596 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.75
RfactorNum. reflection% reflection
Rfree0.2045 3291 5.11 %
Rwork0.1823 --
obs0.1834 64345 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 541 161 3688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083718
X-RAY DIFFRACTIONf_angle_d0.6174941
X-RAY DIFFRACTIONf_dihedral_angle_d15.5312000
X-RAY DIFFRACTIONf_chiral_restr0.041547
X-RAY DIFFRACTIONf_plane_restr0.004590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02860.30531280.30372530X-RAY DIFFRACTION100
2.0286-2.05890.29381460.29152557X-RAY DIFFRACTION100
2.0589-2.0910.24981230.27222561X-RAY DIFFRACTION100
2.091-2.12530.28771380.26512483X-RAY DIFFRACTION100
2.1253-2.1620.27211310.25812593X-RAY DIFFRACTION100
2.162-2.20130.28511350.23622554X-RAY DIFFRACTION100
2.2013-2.24360.19821450.22072540X-RAY DIFFRACTION100
2.2436-2.28940.25931380.21512572X-RAY DIFFRACTION100
2.2894-2.33910.23851390.21242509X-RAY DIFFRACTION100
2.3391-2.39350.23441160.19962556X-RAY DIFFRACTION100
2.3935-2.45340.19581340.20572588X-RAY DIFFRACTION100
2.4534-2.51970.23011170.18792483X-RAY DIFFRACTION100
2.5197-2.59380.20161200.18562601X-RAY DIFFRACTION100
2.5938-2.67750.21981320.17562532X-RAY DIFFRACTION100
2.6775-2.77320.21191420.17722562X-RAY DIFFRACTION100
2.7732-2.88410.20171360.16062542X-RAY DIFFRACTION100
2.8841-3.01530.19531430.16232555X-RAY DIFFRACTION100
3.0153-3.17420.21071710.17262489X-RAY DIFFRACTION100
3.1742-3.37290.1981550.16452532X-RAY DIFFRACTION100
3.3729-3.6330.181210.15792566X-RAY DIFFRACTION100
3.633-3.99810.16721370.14642580X-RAY DIFFRACTION100
3.9981-4.57540.14991460.1432503X-RAY DIFFRACTION100
4.5754-5.75980.18941330.17192563X-RAY DIFFRACTION100
5.7598-33.60030.19941650.17522503X-RAY DIFFRACTION99
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)
11.7636-0.14860.67966.343-2.42024.14020.1558-0.0265-0.0075-0.1045-0.15790.7173-0.0933-0.2058-0.030.2067-0.01870.00360.2641-0.02820.1145-30.9264-5.0637.1906
28.87255.83790.9713.96551.16712.43270.1876-0.0709-1.3692-0.2846-0.00260.68391.4973-0.66360.38960.6491-0.1701-0.05720.2310.02990.5323-30.2138-29.704614.9723
31.4348-0.71910.38367.7227-0.09920.77420.0372-0.0372-0.0514-0.001-0.06720.08880.0919-0.18870.02880.1657-0.02730.00460.1963-0.00190.0783-29.724-4.636317.1235
43.708-4.3373-0.15836.95980.59110.8498-0.0593-0.0449-0.07820.2333-0.0095-0.07840.1418-0.07770.05890.1748-0.0162-0.01370.19340.01240.1018-22.307-9.35523.8941
56.237-7.2813-8.02238.55419.28761.9986-0.3156-1.233-1.561-0.03390.11990.51180.59170.46930.26660.7734-0.02850.05290.45030.1220.6349-19.5279-32.243628.5587
63.44311.3768-0.79085.9219-2.99042.70980.1316-0.2298-0.35720.3312-0.2712-0.06150.5813-0.25160.09550.2888-0.03470.0030.2250.02280.1185-27.3202-12.663329.6614
73.2889-1.31272.54792.126-3.20055.725-0.1695-0.07120.60420.4284-0.0895-0.0133-0.7331-0.10990.12780.24430.0461-0.00930.2208-0.03350.2485-27.531916.587227.2548
84.8705-4.2562.38537.5719-2.09872.3439-0.0952-0.15550.20320.13930.0108-0.0559-0.1641-0.01870.06480.14690.01460.0220.1899-0.00330.0877-19.24127.494325.0575
93.1963-3.2385-1.41346.90552.15332.1644-0.0517-0.1774-0.36540.45660.3348-0.80370.43410.1777-0.16480.22890.0496-0.04880.1889-0.01040.3454-6.7174-21.1221.3551
101.2019-0.01960.38317.31750.43781.89220.04010.0338-0.3514-0.47940.0139-0.3790.31860.1457-0.07090.17370.05360.03950.17240.02210.2017-12.303-13.153315.0025
113.97760.03893.9819.8470.09723.9916-0.4690.43890.9170.20520.1226-0.26-0.72210.92730.2780.3329-0.047-0.01280.33240.03040.2873-8.684116.26216.6861
122.06552.44310.94927.33290.04031.3086-0.14750.1259-0.0618-0.65390.17070.1650.16530.0632-0.05220.26010.00760.02320.2115-0.00550.0972-20.3031-4.90818.3392
137.2935-0.05810.3217.4072.5667.7444-0.14971.1089-0.7571-1.70420.2489-0.15890.6235-0.4378-0.25490.8773-0.17890.0020.3893-0.10140.3786-29.6778-25.47353.0015
143.5222-3.46890.58984.16751.72817.73190.07230.31631.1323-0.9335-0.5513-1.2055-0.15030.260.38470.50450.0910.15580.3730.0291.09565.6754-49.291416.5084
152.2528-2.6762-3.51565.40261.9677.7535-0.3427-0.78221.28080.12510.2341-0.6353-0.52020.4681-0.11140.35740.0523-0.09240.3092-0.22920.93723.8125-53.2125.515
163.7729-3.84391.18036.2031-2.89232.5336-0.0402-1.37110.24810.57310.88190.8656-0.0253-0.3685-0.47240.44680.038-0.03410.35610.00910.6696-3.5295-59.162424.058
173.6131-5.00191.87757.229-1.57124.54950.36860.1136-0.4928-0.7614-0.13540.41881.14440.4792-0.12720.59070.155-0.04850.3620.01280.57975.9532-65.555318.5303
189.5716.6021-0.77078.3274-2.62833.47030.74321.3144-0.2983-1.98380.0871.15380.7469-0.4655-0.9440.88140.1064-0.2130.3150.00720.7198-4.7748-55.566212.8689
194.257-2.57672.04975.9851-2.68911.6384-0.1528-0.0853-0.17360.459-0.0761-0.16390.16830.02720.00780.88540.25680.08940.3963-0.06040.8293-7.9628-47.02413.6506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' (resid 0 through 34)
2X-RAY DIFFRACTION2chain 'A' (resid 35 through 38)
3X-RAY DIFFRACTION3chain 'A' (resid 39 through 73)
4X-RAY DIFFRACTION4chain 'A' (resid 74 through 108)
5X-RAY DIFFRACTION5chain 'A' (resid 109 through 117)
6X-RAY DIFFRACTION6chain 'A' (resid 118 through 137)
7X-RAY DIFFRACTION7chain 'A' (resid 138 through 161)
8X-RAY DIFFRACTION8chain 'A' (resid 162 through 186)
9X-RAY DIFFRACTION9chain 'A' (resid 187 through 208)
10X-RAY DIFFRACTION10chain 'A' (resid 219 through 259)
11X-RAY DIFFRACTION11chain 'A' (resid 260 through 265)
12X-RAY DIFFRACTION12chain 'A' (resid 266 through 292)
13X-RAY DIFFRACTION13chain 'A' (resid 293 through 305)
14X-RAY DIFFRACTION14chain 'A' (resid 1001 through 1021)
15X-RAY DIFFRACTION15chain 'A' (resid 1022 through 1042)
16X-RAY DIFFRACTION16chain 'A' (resid 1061 through 1081)
17X-RAY DIFFRACTION17chain 'A' (resid 1082 through 1093)
18X-RAY DIFFRACTION18chain 'A' (resid 1094 through 1101)
19X-RAY DIFFRACTION19chain 'A' (resid 1102 through 1106)

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