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

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Basic information

Entry
Database: PDB / ID: 5iub
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 12x at 2.1A 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


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / 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 ...positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / 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 / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / 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 / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / 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 / periplasmic space / calmodulin binding / 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-6DV / 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: 2.1 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 13, 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)57,34931
Polymers47,9971
Non-polymers9,35330
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint35 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.276, 179.551, 139.561
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 / Cell line (production host): Tni PRO / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 133 molecules

#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 441.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21F2N9O
#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.: 16 / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→33.62 Å / Num. obs: 27609 / % possible obs: 94.4 % / Redundancy: 5 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.5 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSVERSION January 10, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 2.1→33.621 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 1373 4.98 %Copied from PDB entry 5IU4
Rwork0.1879 ---
obs0.1893 27587 93.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→33.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 509 103 3610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053753
X-RAY DIFFRACTIONf_angle_d0.4215025
X-RAY DIFFRACTIONf_dihedral_angle_d15.9322105
X-RAY DIFFRACTIONf_chiral_restr0.034564
X-RAY DIFFRACTIONf_plane_restr0.003604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.17540.27981130.30852146X-RAY DIFFRACTION78
2.1754-2.26240.29061380.26312449X-RAY DIFFRACTION90
2.2624-2.36540.27431360.22942712X-RAY DIFFRACTION98
2.3654-2.49010.25311620.20942712X-RAY DIFFRACTION98
2.4901-2.6460.23871250.18562716X-RAY DIFFRACTION97
2.646-2.85020.18951650.17952654X-RAY DIFFRACTION97
2.8502-3.13680.23761450.17562664X-RAY DIFFRACTION96
3.1368-3.59030.17481300.17132731X-RAY DIFFRACTION96
3.5903-4.52170.21871360.15692683X-RAY DIFFRACTION95
4.5217-33.62570.19151230.1862747X-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)
12.337-0.42211.36322.06440.33544.1055-0.01250.02540.2641-0.52810.07330.7725-0.1606-0.2294-0.00170.2133-0.0043-0.02250.3043-0.00570.152-30.8741-3.96627.0176
20.0180.0019-0.08170.0022-0.03080.50240.1673-0.1388-0.29950.18340.35750.90880.7434-0.52260.13041.0012-0.2661-0.16930.27630.15960.4581-30.8278-29.843315.3068
31.24310.16650.52850.47450.3951.31460.06390.0014-0.0325-0.113-0.10370.28360.1625-0.2335-00.2288-0.03620.02750.3034-0.00230.1744-29.8454-4.591817.2648
41.8641-0.14920.44030.09290.22321.6208-0.1449-0.0361-0.07040.20380.102-0.0370.2139-0.07770.00010.1855-0.0156-0.0130.22880.01230.1554-22.3539-9.15223.9297
54.6745-0.631-2.90030.15660.40631.7957-0.6299-1.2962-0.81780.30040.20470.05080.91061.12960.07820.8661-0.0480.07420.32920.00710.5293-19.5878-32.026728.7249
60.90190.36240.04840.0932-0.12151.21640.2047-0.2576-0.13710.124-0.40660.2480.4832-0.283-0.01190.3347-0.03970.0010.30650.0270.1767-27.2052-12.029529.8112
70.87-0.15890.65450.16180.01910.8716-0.10840.05190.56630.1965-0.15670.0832-0.4568-0.02030.06590.28620.0494-0.06130.29360.0110.357-27.41116.492727.5336
80.92770.37160.13240.8692-1.09231.20110.0488-0.11190.08060.0329-0.02320.1827-0.0965-0.10450.00020.1890.0181-0.00470.2269-0.01960.195-19.50027.934524.862
90.92330.5655-0.37310.87170.59910.2121-0.0876-0.037-0.49820.44490.1502-0.54210.55840.14290.00040.35340.0504-0.04840.2496-0.01150.3843-7.6027-19.633121.9461
101.3984-0.78520.39181.269-1.06272.20160.09910.0202-0.2999-0.561-0.0841-0.01550.40360.08740.00330.22530.05310.04250.23880.02380.2294-12.5329-13.149814.9776
110.1687-0.08720.26120.39960.24080.6713-0.45230.6683-0.03430.37860.4851-0.3195-0.38670.96880.01640.36260.006-0.07660.340.00250.3603-8.500916.268716.3304
121.92780.41480.02520.6599-1.1051.7117-0.08980.1397-0.1904-0.45120.02470.320.32460.00190.00030.2551-0.01070.02260.2729-0.01120.2064-20.4432-4.89668.3259
130.85410.7325-0.38741.6009-0.79660.7908-0.13830.0597-0.9481-1.11340.3556-0.63061.1787-0.1402-0.080.9605-0.1901-0.04130.4357-0.11920.4316-29.9901-25.26013.4134
140.7215-0.29060.5351.16361.11682.7271-0.3740.0398-0.1825-1.1566-0.4885-1.6568-0.50420.2865-0.2420.66250.0280.36730.33570.1551.3265.7028-48.936716.6169
150.04830.1832-0.210.747-1.43912.675-0.2383-0.23460.31920.2147-0.9151-1.5156-0.74870.6063-0.32560.54020.0618-0.07240.4061-0.14581.46673.9106-52.708125.5719
166.1153-2.16141.02133.0821-1.04152.1561-0.2292-1.75570.95330.6380.87670.32230.0054-0.91350.11770.5872-0.0079-0.04880.45980.1030.9286-5.1119-57.839723.6004
170.0511-0.05730.02290.04230.05810.12540.25540.42130.0972-0.3495-0.3151-0.44620.23770.6681-0.00020.95940.25670.19450.57160.06671.17466.271-65.079518.6545
182.39830.71060.60891.17240.59191.04060.10910.934-0.7559-1.35770.49350.48020.0622-0.45160.64171.35270.272-0.00910.30020.08090.9701-4.5399-55.32312.6729
190.8643-0.64790.32680.6740.19381.5076-0.2392-1.00710.1994-0.02780.4613-0.6696-0.18-0.1004-0.19371.23110.43410.05390.5323-0.30250.7824-7.8726-46.896413.5351
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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