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- PDB-5iu4: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5iu4
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with ZM241385 at 1.7A 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 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 / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 Inititative 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 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 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 1.4Nov 20, 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)57,33632
Polymers47,9971
Non-polymers9,33931
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint48 kcal/mol
Surface area20630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.428, 179.599, 139.847
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, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, ...Mutation: A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, 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) / Strain (production host): Tni PRO / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 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-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#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.: 20 / 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.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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 / 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: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2014 / 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: 1.72→33.73 Å / Num. obs: 49406 / % possible obs: 93.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.2
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 1.5 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSVersion January 10, 2014data reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 4EIY

4eiy


Resolution: 1.72→33.733 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 4682 4.94 %Random
Rwork0.1671 ---
obs0.1687 49292 93.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→33.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 499 164 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093755
X-RAY DIFFRACTIONf_angle_d0.8225041
X-RAY DIFFRACTIONf_dihedral_angle_d15.442056
X-RAY DIFFRACTIONf_chiral_restr0.049571
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.73960.35111740.31372982X-RAY DIFFRACTION94
1.7396-1.760.29211530.30452984X-RAY DIFFRACTION92
1.76-1.78150.35431430.2813018X-RAY DIFFRACTION92
1.7815-1.8040.28881720.27033032X-RAY DIFFRACTION94
1.804-1.82780.28671620.24782951X-RAY DIFFRACTION94
1.8278-1.85280.27181580.24223034X-RAY DIFFRACTION93
1.8528-1.87930.27221600.23923060X-RAY DIFFRACTION94
1.8793-1.90730.21941240.23142963X-RAY DIFFRACTION93
1.9073-1.93710.26061520.2093024X-RAY DIFFRACTION93
1.9371-1.96890.23471430.20843088X-RAY DIFFRACTION94
1.9689-2.00280.22861630.1892923X-RAY DIFFRACTION93
2.0028-2.03920.19521710.18623018X-RAY DIFFRACTION93
2.0392-2.07850.19711690.17973067X-RAY DIFFRACTION93
2.0785-2.12090.23461720.16963000X-RAY DIFFRACTION95
2.1209-2.1670.17981470.16123027X-RAY DIFFRACTION93
2.167-2.21740.1831780.15672947X-RAY DIFFRACTION92
2.2174-2.27280.16211520.15523043X-RAY DIFFRACTION95
2.2728-2.33430.23941500.14813068X-RAY DIFFRACTION93
2.3343-2.40290.22211450.14832964X-RAY DIFFRACTION93
2.4029-2.48050.19871840.14392979X-RAY DIFFRACTION91
2.4805-2.56910.17161450.14152990X-RAY DIFFRACTION93
2.5691-2.67190.13611380.13593065X-RAY DIFFRACTION94
2.6719-2.79350.18081870.13983000X-RAY DIFFRACTION93
2.7935-2.94070.19541850.14382940X-RAY DIFFRACTION93
2.9407-3.12480.16371460.14832959X-RAY DIFFRACTION92
3.1248-3.36590.16851330.15283041X-RAY DIFFRACTION93
3.3659-3.70420.18651690.14362959X-RAY DIFFRACTION92
3.7042-4.23930.18231350.14413032X-RAY DIFFRACTION93
4.2393-5.33770.1771490.15363004X-RAY DIFFRACTION92
5.3377-33.73970.19621230.17482960X-RAY DIFFRACTION91
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)
11.91460.38610.12222.7392-1.66253.80130.04730.00990.027-0.2369-0.02590.2594-0.0931-0.2587-0.06870.1692-0.0065-0.01470.2247-0.01750.0819-30.8007-3.88156.9616
20.79180.9101-0.85191.0439-0.97820.9159-0.0687-0.0205-0.393-0.01830.09220.45620.3739-0.1280.31410.7543-0.2586-0.13710.17810.14770.4939-30.6342-29.93715.201
31.5264-0.41250.65453.7014-0.02771.37210.0702-0.0492-0.0147-0.1392-0.13930.20030.1223-0.22620.05660.0855-0.02270.01820.1904-0.00810.0616-29.8145-4.228317.236
42.8681-3.1752-0.21987.21170.64061.0036-0.0905-0.0824-0.04350.23770.0429-0.03960.1361-0.06230.02380.1075-0.0127-0.01390.17870.00560.0614-22.4813-8.662324.0245
55.5329-5.3276-4.14545.16834.19214.1774-0.6063-0.795-1.35770.48580.13340.69571.11960.37620.29650.6535-0.02560.04430.30730.14550.5034-19.4789-32.02528.6784
62.54550.2276-0.02292.6173-1.03571.50910.0555-0.2574-0.25760.287-0.1530.020.4431-0.1290.06660.2265-0.0233-0.00020.21180.03680.0998-27.1869-12.116429.813
73.3337-1.98091.95276.7864-3.97953.9057-0.0172-0.11170.46390.0869-0.09330.2813-0.4383-0.10180.07950.18760.0545-0.02430.1797-0.04130.1786-27.729116.73727.0944
82.0145-0.92590.5573.1675-0.9511.99730.0441-0.02330.1247-0.0366-0.11120.084-0.1330.00440.05170.08610.0131-0.0040.157-0.01540.0908-19.33687.696725.1141
92.7292-1.3657-1.15341.14031.50582.5168-0.1091-0.1327-0.38850.15160.208-0.1880.33010.2181-0.14270.16470.0505-0.02980.15860.00330.2448-7.2289-19.831121.9482
100.95610.11310.4884.60270.1011.23490.08070.015-0.2637-0.29970.0217-0.2080.27850.1115-0.04910.14210.04210.02060.14530.00610.1587-12.4637-13.093115.0019
114.7674-2.30242.36734.2645-0.36254.2928-0.29390.20040.57050.07980.0417-0.5157-0.56261.0450.38540.2002-0.0731-0.02060.22950.0570.2463-8.620316.400816.3878
121.61811.71580.11125.4306-0.24092.0283-0.10860.1469-0.088-0.32910.14390.13880.1912-0.0663-0.04480.14870.00990.00330.1991-0.00790.0937-20.4195-4.26338.4043
138.23391.05441.11745.31742.05785.87130.14760.9047-0.9983-1.06010.1538-0.05530.9278-0.3134-0.29990.7766-0.1535-0.04160.3745-0.06690.3005-29.7979-25.333.3924
146.2923-5.0437-0.58744.97331.19543.1542-0.0323-0.03450.2382-0.6256-0.539-1.1795-0.12930.23290.15720.42290.18020.14070.21920.01691.11915.8039-48.974216.6326
153.3623-2.937-2.18084.5428-0.63934.7675-0.3952-0.6951.29170.2235-0.093-0.3761-0.6880.66450.18780.36940.0358-0.15840.4471-0.20591.0213.9158-52.959125.6483
165.47340.23451.23322.66521.07158.79440.0326-0.63470.20850.09060.50251.1492-0.0863-0.5943-0.48980.3415-0.01120.02360.22590.08630.6625-5.1127-57.969123.5501
176.1828-3.94852.01746.6258-0.12052.6848-0.2417-0.1371-0.1278-0.4545-0.0607-0.1690.19410.16790.06920.66570.26770.21290.17880.05330.81466.1482-65.286218.5885
181.55030.73961.64274.8455-0.92587.05730.20650.5629-0.3152-1.2986-0.04110.62080.06920.1132-0.11170.76570.1227-0.09990.25510.04990.6686-4.448-55.375212.7478
195.4455-2.43770.62477.4421-1.97541.2946-0.0596-0.0451-0.1569-0.2196-0.0066-0.2619-0.0399-0.00090.05770.77450.2985-0.02170.342-0.0720.7601-7.797-46.840713.5645
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 1058 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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