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- PDB-5iu8: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5iu8
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with compound 12f at 2.0A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-protein-coupled receptor / integral membrane protein / chimera / thermostabilizing mutationsm
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 / NGF-independant TRKA activation ...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 / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / : / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / synaptic transmission, glutamatergic / central nervous system development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / positive regulation of apoptotic signaling pathway / electron transport chain / 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 / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / heme binding / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / 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-6DZ / CHOLESTEROL / HEPTANE-1,2,3-TRIOL / 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: 2.002 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 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Jan 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

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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)57,56433
Polymers47,9971
Non-polymers9,56732
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint16 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.312, 179.537, 139.994
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 , 8 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-6DZ / 2-(furan-2-yl)-N~5~-[2-(4-methylpiperazin-1-yl)ethyl][1,2,4]triazolo[1,5-a][1,3,5]triazine-5,7-diamine


Mass: 343.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N9O
#4: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#5: Chemical
ChemComp-CLR / CHOLESTEROL


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


Mass: 282.461 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


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


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#9: 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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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, 33.5% PEG400, 0.5% (v/v) 1,2,3-heptanetriol

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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: Mar 4, 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: 2→33.67 Å / Num. obs: 33982 / % possible obs: 99.7 % / Redundancy: 8 % / Biso Wilson estimate: 24.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.7
Reflection shellResolution: 2→2.05 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.185 / Mean I/σ(I) obs: 1.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSVERSION November 3, 2014data reduction
Aimlessversion 0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IU4

5iu4


Resolution: 2.002→33.668 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 1703 5.02 %copied from PDB entry 5IU4
Rwork0.1808 ---
obs0.1817 33943 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→33.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 542 157 3689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033752
X-RAY DIFFRACTIONf_angle_d0.45018
X-RAY DIFFRACTIONf_dihedral_angle_d15.6132046
X-RAY DIFFRACTIONf_chiral_restr0.034565
X-RAY DIFFRACTIONf_plane_restr0.003596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.06090.2821570.24722641X-RAY DIFFRACTION100
2.0609-2.12750.30461430.22512620X-RAY DIFFRACTION100
2.1275-2.20350.21151490.20812677X-RAY DIFFRACTION100
2.2035-2.29170.20771350.19322658X-RAY DIFFRACTION100
2.2917-2.3960.24411370.18212633X-RAY DIFFRACTION100
2.396-2.52220.24181510.18072651X-RAY DIFFRACTION100
2.5222-2.68020.17681260.16812697X-RAY DIFFRACTION100
2.6802-2.8870.17681790.16652652X-RAY DIFFRACTION100
2.887-3.17740.17161270.17252696X-RAY DIFFRACTION100
3.1774-3.63670.1651340.16652713X-RAY DIFFRACTION99
3.6367-4.580.18911400.15762737X-RAY DIFFRACTION99
4.58-33.67270.18451250.19272865X-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)
11.48520.1548-0.06667.562-3.62013.83330.05780.0168-0.0015-0.27070.0180.2996-0.0503-0.1934-0.05750.15230.0009-0.00630.2114-0.00740.066-30.5668-3.6256.8351
25.01672.0262-0.24960.8591-0.41132.38490.2093-0.2271-1.05510.3460.05270.87881.4033-0.480.43190.4406-0.1171-0.02550.25090.09260.4616-30.537-30.003815.1089
31.1357-1.17330.61978.515-0.06731.06990.0638-0.0335-0.0629-0.0104-0.10870.24690.0679-0.1420.01410.0989-0.02510.00870.17210.00640.0549-29.7495-4.745117.2753
43.4187-4.4148-0.14138.87250.6790.8428-0.1365-0.0794-0.05340.30470.1204-0.01970.1847-0.06850.01270.1274-0.0223-0.00480.1790.00910.0545-22.4222-8.759124.0888
55.7359-0.6036-5.46243.97494.1378.4402-0.3781-1.3457-1.61170.64330.40220.54860.96970.37670.08440.6101-0.04030.00260.320.11120.4743-19.4143-32.114128.7588
61.77711.2611-0.26616.1675-1.91352.29220.0652-0.2318-0.14870.254-0.15660.05540.3977-0.14110.0570.1989-0.0240.00360.19860.02410.0919-27.2683-12.300329.7344
72.8374-2.20311.85646.923-2.76553.98-0.1846-0.03170.52760.2811-0.03680.1031-0.5422-0.06320.16210.19780.0512-0.03420.1821-0.02830.1957-27.47316.359227.691
82.9445-2.25451.41285.0425-1.36632.3103-0.0225-0.09870.1393-0.0121-0.0045-0.0333-0.10670.00620.02610.1130.00550.0090.141-0.00330.068-19.27747.590725.1833
92.6781-1.9908-1.30255.66441.77042.1694-0.1783-0.101-0.30210.52780.2879-0.5070.45060.2365-0.06330.19490.0473-0.02960.1692-0.0150.2377-7.0939-19.907822.0487
100.8924-0.01540.31266.61810.68971.55480.08180.0058-0.2539-0.3888-0.0256-0.20380.23610.1165-0.03310.13130.04310.02070.15670.01840.1512-12.2838-13.142615.1605
115.18091.98765.23057.59212.44435.3071-0.85140.63820.9117-0.48180.20130.1068-0.64610.64580.8470.2443-0.0503-0.03250.23840.03560.2767-8.602316.271916.3679
121.96171.5510.6014.87650.0961.328-0.08660.11660.0855-0.50270.03730.26880.06490.07720.04210.175-0.00490.01140.20360.02050.0483-20.348-4.99678.4207
131.79060.3480.4590.9231-0.5971.8189-0.0464-0.0001-0.0428-0.14080.17390.00070.1259-0.11390.02520.1087-0.0170.0540.23030.0130.0302-26.5588-5.718715.143
142.9063-4.51-1.13027.66982.52462.7759-0.2797-0.03060.1747-0.7072-0.2774-1.4124-0.12290.2230.28380.50220.16310.2460.31570.10391.17795.748-49.117616.5373
150.7955-0.7932-1.57832.8104-1.71788.4981-0.3911-0.83851.50410.001-0.4238-1.0055-0.22750.37020.61340.36920.0302-0.0650.3731-0.16921.14243.9672-53.019625.5601
167.71751.7782.51324.01081.70069.0274-0.2229-0.79260.03630.66940.67170.8205-0.2099-0.7186-0.41730.4173-0.02010.02230.27730.10370.5993-4.5158-58.491823.7278
176.8766-4.44661.15229.0686-2.02615.5440.43740.4585-0.4851-1.0645-0.7176-0.17560.91721.1370.20170.67110.13690.16960.38720.02290.64376.0814-65.415518.5296
182.00090.8669-1.86823.2268-2.85997.0950.76871.2156-0.9952-2.5661-0.60720.3660.5188-0.0195-0.30910.97760.154-0.03170.32680.0430.7036-4.607-55.443512.8122
191.3826-1.39210.80944.65350.26950.8366-0.2029-0.1895-0.28370.09520.1342-0.32640.0075-0.02990.04571.02680.4365-0.01540.5401-0.18630.7439-7.7841-46.933413.6576
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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