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- PDB-5iu7: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5iu7
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 12c at 1.9A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-protein-coupled receptor / integral membrane protein / chimera / 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
Chem-6DY / CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (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: 1.9 Å
AuthorsSegala, E. / Guo, D. / Cheng, R.K.Y. / Bortolato, A. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Heitman, L.H. / Ijzerman, A.P. / Marshall, F.H. / Cooke, R.M.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative Joint Undertaking115366
CitationJournal: J.Med.Chem. / Year: 2016
Title: Controlling the Dissociation of Ligands from the Adenosine A2A Receptor through Modulation of Salt Bridge Strength.
Authors: Segala, E. / Guo, D. / Cheng, R.K. / Bortolato, A. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Heitman, L.H. / IJzerman, A.P. / Marshall, F.H. / Cooke, R.M.
History
DepositionMar 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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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)57,90733
Polymers47,9971
Non-polymers9,91132
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint47 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.384, 180.036, 139.835
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: 47996.746 Da / Num. of mol.: 1
Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, ...Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A
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) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 189 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-6DY / 2-(furan-2-yl)-N~5~-[2-(4-phenylpiperidin-1-yl)ethyl][1,2,4]triazolo[1,5-a][1,3,5]triazine-5,7-diamine


Mass: 404.468 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H24N8O
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.58 Å3/Da / Density % sol: 52.36 % / Description: rectangular
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.lM tri-sodium citrate pH 5.3-5.4, 0.05M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol
PH range: 5.3-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2015 / Details: (double) KB mirror pair
RadiationMonochromator: Double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→33.71 Å / Num. obs: 39593 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.007 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSVERSION March 1, 2015data reduction
Aimlessversion 0.5.9data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 1.9→33.708 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 19.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 3726 4.95 %
Rwork0.1703 --
obs0.1717 39555 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 538 157 3726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013863
X-RAY DIFFRACTIONf_angle_d0.8115186
X-RAY DIFFRACTIONf_dihedral_angle_d15.8652142
X-RAY DIFFRACTIONf_chiral_restr0.05585
X-RAY DIFFRACTIONf_plane_restr0.005622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.92410.31461110.29732694X-RAY DIFFRACTION100
1.9241-1.94940.34061340.28892681X-RAY DIFFRACTION100
1.9494-1.97610.3641260.2772686X-RAY DIFFRACTION100
1.9761-2.00440.28541510.26422637X-RAY DIFFRACTION100
2.0044-2.03430.2951460.2412646X-RAY DIFFRACTION100
2.0343-2.06610.24871700.23482658X-RAY DIFFRACTION100
2.0661-2.09990.26531330.22482644X-RAY DIFFRACTION99
2.0999-2.13610.23661550.21042633X-RAY DIFFRACTION100
2.1361-2.1750.22951160.20582678X-RAY DIFFRACTION99
2.175-2.21680.20911600.19662586X-RAY DIFFRACTION99
2.2168-2.2620.18311410.17962653X-RAY DIFFRACTION99
2.262-2.31120.22531210.17522697X-RAY DIFFRACTION100
2.3112-2.3650.25231460.16882610X-RAY DIFFRACTION99
2.365-2.42410.2141200.15862689X-RAY DIFFRACTION99
2.4241-2.48960.20761880.15842587X-RAY DIFFRACTION99
2.4896-2.56280.17811270.15062660X-RAY DIFFRACTION100
2.5628-2.64550.15471290.14842676X-RAY DIFFRACTION100
2.6455-2.740.15671430.13892617X-RAY DIFFRACTION100
2.74-2.84970.16411690.14032666X-RAY DIFFRACTION100
2.8497-2.97930.17291670.13782615X-RAY DIFFRACTION99
2.9793-3.13630.15351150.14782643X-RAY DIFFRACTION100
3.1363-3.33260.17581250.14512705X-RAY DIFFRACTION100
3.3326-3.58970.17441330.14862669X-RAY DIFFRACTION100
3.5897-3.95040.15841330.14542624X-RAY DIFFRACTION99
3.9504-4.52090.18991300.14542630X-RAY DIFFRACTION99
4.5209-5.69140.1881270.16932650X-RAY DIFFRACTION98
5.6914-33.7130.1921100.18272611X-RAY DIFFRACTION97
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)
11.5243-0.11570.06627.6265-2.31183.29970.1092-0.0257-0.0073-0.303-0.05740.4231-0.0378-0.1848-0.01870.1752-0.015-0.01190.2006-0.00980.0878-11.3183-4.70357.1391
29.01534.21680.63991.98460.32090.08530.005-0.0696-1.4862-0.11910.14390.55031.2678-0.5444-0.0690.6412-0.1529-0.07050.27590.07770.4597-10.8679-30.040615.1594
31.7059-1.26350.54277.4395-0.02261.18030.0646-0.0525-0.0584-0.0428-0.04060.17780.0912-0.1787-0.03990.1085-0.02110.01530.17230.010.0572-10.199-4.320217.1719
43.3533-4.0424-0.21197.93380.78850.921-0.0662-0.1164-0.0410.19580.0531-0.07530.1594-0.07880.0230.1447-0.0175-0.0210.18250.01080.0748-2.4406-9.362124.0002
54.934-5.6801-0.88749.52164.0414.0907-0.6799-1.0615-1.41591.21830.14550.28580.90620.67840.68610.7043-0.04020.03590.41190.14730.51350.1727-32.204928.661
62.38861.3334-0.53367.7017-2.12762.27680.0693-0.1589-0.23610.3158-0.11010.04810.5035-0.20820.06190.2388-0.0365-0.00040.21420.02860.1066-7.5946-12.353529.6952
73.0385-1.82651.86372.1817-2.98724.847-0.105-0.14290.60130.2489-0.0686-0.0445-0.7239-0.08970.09390.28530.0527-0.03180.215-0.03350.2596-7.973716.713227.1974
84.511-3.92681.1797.3394-1.46182.74790.01110.00650.23420.0412-0.1046-0.1238-0.16910.02230.06710.1123-0.00980.00970.15240.00590.08810.41297.608625.1851
92.9899-1.5878-1.46411.53911.94972.685-0.0856-0.1488-0.41360.28690.2162-0.32410.40880.1867-0.20040.19830.0368-0.04180.18890.00950.290412.6758-20.602221.6939
100.9278-0.01930.36296.80010.42291.39020.07320.0257-0.287-0.35780.0301-0.29970.30170.1776-0.0720.17160.05530.0160.17040.0210.18137.3215-13.39914.9511
114.9063-2.35513.07458.59431.44733.0717-0.52080.49440.6104-0.21610.3497-0.3791-0.63120.93010.12940.2586-0.05760.03730.31040.06620.260611.149416.30516.4813
121.60962.15760.5497.3567-0.26041.5022-0.03630.12050.014-0.38240.01080.16750.11230.0729-0.00680.16150.01020.00940.18820.01040.0804-0.6061-4.62348.3494
137.27310.25312.90997.42710.66557.3775-0.03610.782-0.6891-1.21750.31810.39920.695-0.3446-0.32420.6845-0.1421-0.03660.3298-0.05090.3122-11.309-25.03133.212
146.0261-6.75860.3789.23892.62595.6785-0.0836-0.03080.6351-1.0692-0.3671-1.0822-0.03660.07290.43810.48570.12460.14980.38040.09021.07925.4454-49.156616.691
154.2111-3.3254-4.11273.37891.51158.0352-0.3866-1.2921.190.19640.0229-0.8864-0.49790.63990.40180.43770.0234-0.11570.4567-0.1490.938423.6603-53.14325.8393
163.7448-0.93412.39536.19221.1572.5897-0.2112-1.27810.05110.41310.65440.84360.165-0.4437-0.47150.49080.04190.02610.42490.13790.673615.1798-58.558323.7831
173.4269-3.34512.71835.5764-3.23352.7925-0.1459-0.2154-0.1017-0.34960.05220.14850.65210.34260.22930.74840.21930.19110.42080.10840.882925.8411-65.412518.7479
186.37282.67343.13213.7939-0.92426.91880.66190.6689-0.6906-1.5815-0.1070.72270.97390.2691-0.47830.84430.1671-0.06960.35090.06070.827715.0829-55.521412.9657
196.69581.40182.38979.6403-3.15397.8340.05720.1088-0.6455-0.9851-0.3012-0.5631-0.2014-0.05310.20940.82380.2289-0.05730.3593-0.03920.578311.8705-46.997413.6956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' (resid -1 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 307)
14X-RAY DIFFRACTION14chain 'A' (resid 1001 through 1021)
15X-RAY DIFFRACTION15chain 'A' (resid 1022 through 1042)
16X-RAY DIFFRACTION16chain 'A' (resid 1059 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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