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- PDB-6gt3: Crystal Structure of the A2A-StaR2-bRIL562 in complex with AZD463... -

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Basic information

Entry
Database: PDB / ID: 6gt3
TitleCrystal Structure of the A2A-StaR2-bRIL562 in complex with AZD4635 at 2.0A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / 7TM / GPCR / SIGNALLING PROTEIN
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
CHOLESTEROL / Chem-F9Q / OLEIC ACID / (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 Å
AuthorsBorodovsky, A. / Wang, Y. / Deng, N. / Ye, M. / Stephen, T.L. / Goodwin, K. / Goodwin, R. / Strittmatter, N. / Shaw, J. / Sachsenmeier, K. ...Borodovsky, A. / Wang, Y. / Deng, N. / Ye, M. / Stephen, T.L. / Goodwin, K. / Goodwin, R. / Strittmatter, N. / Shaw, J. / Sachsenmeier, K. / Clarke, J.D. / Hay, C. / Reimer, C. / Andrews, S.P. / Brown, G.A. / Congreve, M. / Cheng, R.K.Y. / Dore, A.S. / Mason, J.S. / Marshall, F.H. / Weir, M.P. / Lyne, P. / Woessner, R.
CitationJournal: J Immunother Cancer / Year: 2020
Title: Small molecule AZD4635 inhibitor of A2AR signaling rescues immune cell function including CD103+ dendritic cells enhancing anti-tumor immunity
Authors: Borodovsky, A. / Barbon, C.M. / Wang, Y. / Ye, M. / Prickett, L. / Chandra, D. / Shaw, J. / Deng, N. / Sachsenmeier, K. / Clarke, J.D. / Linghu, B. / Brown, G.A. / Brown, J. / Congreve, M. / ...Authors: Borodovsky, A. / Barbon, C.M. / Wang, Y. / Ye, M. / Prickett, L. / Chandra, D. / Shaw, J. / Deng, N. / Sachsenmeier, K. / Clarke, J.D. / Linghu, B. / Brown, G.A. / Brown, J. / Congreve, M. / Cheng, R.K.Y. / Dore, A.S. / Hurrell, E. / Shao, W. / Woessner, R. / Reimer, C. / Drew, L. / Fawell, S. / Schuller, A.G. / Mele, D.A.
History
DepositionJun 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Jan 17, 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 1.3Oct 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)57,29831
Polymers47,9971
Non-polymers9,30130
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, MONDISPERSE PEAK
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint47 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.550, 179.714, 140.776
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, M1007W, H1102I, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, H1102I, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, ...Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, H1102I, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, H1102I, L235A, V239A, S277A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, H1102I, 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 166 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-F9Q / 6-(2-chloranyl-6-methyl-pyridin-4-yl)-5-(4-fluorophenyl)-1,2,4-triazin-3-amine


Mass: 315.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClFN5 / Feature type: SUBJECT OF INVESTIGATION
#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.: 15 / 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.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.11 Å3/Da / Density % sol: 41.75 % / Description: 0.060-0.080 MM LONG PLATE-SHAPED CRYSTALS
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 5.3
Details: 0.1 M TRI-SODIUM CITRATE PH 5.3-5.4, 0.05 M SODIUM THIOCYANATE, 29-32% PEG400, 2%(V/V) 2,5-HEXANEDIOL
PH range: 5.3-5.4 / Temp details: None

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: None
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 10, 2015 / Details: NULL
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→33.86 Å / Num. obs: 33848 / % possible obs: 97.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 1.35

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSv1.0data reduction
Aimlessv1.0data scaling
PHASERv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 2→33.8 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.76
RfactorNum. reflection% reflection
Rfree0.2009 1710 5.05 %
Rwork0.1826 --
obs0.1835 33848 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 511 136 3645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033756
X-RAY DIFFRACTIONf_angle_d0.985023
X-RAY DIFFRACTIONf_dihedral_angle_d10.1531195
X-RAY DIFFRACTIONf_chiral_restr0.022555
X-RAY DIFFRACTIONf_plane_restr0.003617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05890.29581520.25712568X-RAY DIFFRACTION97
2.0589-2.12530.23521490.22962610X-RAY DIFFRACTION97
2.1253-2.20130.21361370.20982661X-RAY DIFFRACTION97
2.2013-2.28940.20781480.19732607X-RAY DIFFRACTION98
2.2894-2.39360.25411360.18772648X-RAY DIFFRACTION98
2.3936-2.51970.23581570.17862647X-RAY DIFFRACTION98
2.5197-2.67750.20811280.17252668X-RAY DIFFRACTION98
2.6775-2.88420.18061690.16972624X-RAY DIFFRACTION97
2.8842-3.17420.19371340.17632721X-RAY DIFFRACTION98
3.1742-3.63310.16511360.16972722X-RAY DIFFRACTION99
3.6331-4.57550.19841370.15952759X-RAY DIFFRACTION99
4.5755-33.86720.181270.1922903X-RAY DIFFRACTION98
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)
11.7118-0.09640.75786.6432-1.75314.5414-0.02660.07050.0629-0.38280.19130.6355-0.2201-0.4078-0.10350.1877-0.0008-0.02340.29430.00320.1014-30.9004-4.19257.088
27.78366.72182.82997.48613.16341.34920.9466-0.3452-1.0817-0.62350.09320.83741.2919-0.8739-0.86590.6344-0.1569-0.11720.3170.09130.4063-30.7382-29.824315.485
31.2984-0.97520.87196.9527-0.73831.65670.0424-0.07510.006-0.2762-0.01640.23250.039-0.2251-0.04860.1065-0.02320.01820.24490.00030.0861-29.8647-4.066317.2462
42.8504-2.75240.04565.81780.60061.1133-0.1901-0.21920.00910.14610.2526-0.03240.1816-0.1791-0.03590.1158-0.0097-0.01410.2530.01330.0769-22.4798-8.956524.1185
56.6191-1.8065-4.75825.17933.61684.5402-0.5431-1.5956-1.41480.60340.41470.77631.3810.40770.10780.7758-0.0230.06580.41830.0990.5308-19.5518-31.964528.9462
62.54261.3515-0.03497.0781-0.27591.61010.1146-0.3013-0.19090.4106-0.28470.09310.4081-0.13940.17430.2101-0.02030.01250.2810.04410.1088-27.2533-11.951529.9332
74.8754-2.24582.46046.8784-3.82784.7192-0.0895-0.01090.69320.3108-0.09620.37-0.7299-0.09150.13840.23660.0665-0.03410.2531-0.03770.2645-27.54916.692127.6966
85.3262-2.95870.55455.1036-0.45351.9390.08110.07390.2348-0.1469-0.09470.0516-0.1686-0.07650.00120.11680.0103-0.00130.20310.00070.1098-19.30027.834325.3217
93.4384-1.8797-0.80411.66111.61832.4886-0.1221-0.0969-0.2940.44190.2715-0.4590.45380.357-0.11150.19160.0616-0.01950.21210.01670.2609-7.5081-19.475322.2137
100.9460.54490.71995.12570.02471.82340.04720.02-0.2417-0.490.0918-0.28240.31370.2016-0.07380.12980.06150.03780.19550.01940.1747-12.4221-12.672215.185
115.56374.325.44943.54944.33715.4642-0.70281.1610.33520.3040.4845-0.7663-0.40131.49270.21790.3652-0.0497-0.03410.39040.07110.3968-8.658716.584916.4736
122.45442.35910.40245.9590.31843.2349-0.22820.3362-0.1174-0.53860.2740.2560.2287-0.0033-0.05080.19390.01640.00760.2742-0.0120.121-20.5739-4.80658.3846
132.16090.83690.62631.9273-0.50332.607-0.0793-0.1219-0.0502-0.09680.11960.0890.2403-0.2125-0.04230.1847-0.00880.07110.4048-0.00570.1327-27.2934-5.761215.7654
145.4012-5.3394-1.67166.94472.18174.0326-0.3514-0.0940.1323-0.6121-0.3679-1.1952-0.26880.4677-0.08110.36760.26190.33150.35360.03691.50585.6833-48.929316.837
152.7399-2.4786-3.08965.3077-1.25848.9639-0.4866-0.88221.54920.2883-0.3714-0.5057-0.5940.23120.57150.38240.0447-0.15830.4237-0.20971.10444.0083-52.795825.696
168.4759-0.93133.13014.40931.9018.13870.173-1.5334-0.30030.41650.80471.18780.0657-1.1393-0.86550.44640.0093-0.00910.46040.17290.8098-5.0653-57.851423.6785
174.5933-4.15911.21434.4722-1.41357.7296-0.10630.3977-0.087-1.0129-0.7318-0.56210.71760.32580.86410.63830.1560.08770.36810.00740.83676.2813-65.173118.6414
186.72645.1348-0.74754.2712-0.61539.42830.69041.2585-0.4179-1.545-0.11210.77450.50230.0429-0.5090.80990.1775-0.00030.38180.08390.7501-4.3936-55.24612.7724
196.7424-3.84125.08686.5864-5.91835.9133-0.6877-0.9834-0.5552-0.43780.1026-0.5069-0.9333-0.78690.48310.9310.31530.00630.4656-0.10930.6702-7.7786-46.805213.681
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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