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- PDB-7px4: Crystal structure of the adenosine A2A receptor (A2A-PSB1-bRIL) i... -

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Basic information

Entry
Database: PDB / ID: 7px4
TitleCrystal structure of the adenosine A2A receptor (A2A-PSB1-bRIL) in complex with preladenant conjugate PSB-2113
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / GPCR / A2A / G protein-coupled receptor / adenosine receptor / preladenant
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 / 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 / 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
Preladenant conjugate PSB-2113 / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsClaff, T. / Klapschinski, T.A. / Tiruttani Subhramanyam, U.K. / Vaassen, V.J. / Schlegel, J.G. / Vielmuth, C. / Voss, J.H. / Labahn, J. / Muller, C.E.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1328 Germany
German Research Foundation (DFG)FOR2327 Germany
German Federal Ministry for Education and Research Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates.
Authors: Claff, T. / Klapschinski, T.A. / Tiruttani Subhramanyam, U.K. / Vaassen, V.J. / Schlegel, J.G. / Vielmuth, C. / Voss, J.H. / Labahn, J. / Muller, C.E.
History
DepositionOct 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)60,59536
Polymers50,0161
Non-polymers10,57935
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint111 kcal/mol
Surface area21740 Å2
Unit cell
Length a, b, c (Å)39.600, 180.262, 139.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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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: 50016.379 Da / Num. of mol.: 1 / Mutation: S91K
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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 266 molecules

#2: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#3: Chemical ChemComp-8E2 / Preladenant conjugate PSB-2113 / ~{tert}-butyl 2-[2-[2-[2-[2-[2-[4-[4-[2-[7-azanyl-4-(furan-2-yl)-3,5,6,8,10,11-hexazatricyclo[7.3.0.0^{2,6}]dodeca-1(9),2,4,7,11-pentaen-10-yl]ethyl]piperazin-1-yl]phenoxy]ethanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]ethanoate


Mass: 792.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H52N10O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 24% (v/v) PEG-400 (polyethylene glycol 400, average molecular weight 400), 10-30 mM sodium thiocyanate, 100 mM sodium citrate pH 5.2, and 2% (v/v) 2,5-hexanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2020
RadiationMonochromator: Double crystal (Si-111 and Si-113 reflection)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.25→45.06 Å / Num. obs: 24297 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 35.86 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.69
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 1.345 / Num. unique obs: 2375 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 2.25→42.88 Å / SU ML: 0.3133 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.3685
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 1082 4.45 %
Rwork0.1962 23209 -
obs0.1981 24291 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.97 Å2
Refinement stepCycle: LAST / Resolution: 2.25→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 578 231 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253628
X-RAY DIFFRACTIONf_angle_d0.5014805
X-RAY DIFFRACTIONf_chiral_restr0.0364526
X-RAY DIFFRACTIONf_plane_restr0.0031558
X-RAY DIFFRACTIONf_dihedral_angle_d13.53591421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.350.37271290.29332799X-RAY DIFFRACTION97.15
2.35-2.470.24961340.26532858X-RAY DIFFRACTION99.93
2.47-2.630.27861340.23052875X-RAY DIFFRACTION100
2.63-2.830.28041340.21932865X-RAY DIFFRACTION99.97
2.83-3.120.24121350.19932884X-RAY DIFFRACTION99.9
3.12-3.570.20571360.18752917X-RAY DIFFRACTION100
3.57-4.490.20281370.15772942X-RAY DIFFRACTION99.97
4.5-42.880.24541430.18543069X-RAY DIFFRACTION99.6
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)
10.978430021238-0.122929565310.2265496724011.128140192690.1272857117861.19226208337-0.0344426640572-0.04476076470670.0166309186204-0.03354510081810.02680350968220.0405170710543-0.0271193289188-0.0533277856163-0.0001122663412110.223853938003-0.009025653092840.0115644367660.2655775269150.01023690914890.20741638472313.644716889-3.8889532260820.7359669215
20.0489209678335-0.533442246626-0.02725636384541.42706667004-0.1419650368980.128654447525-0.014939104238-0.162399784596-0.372709028678-0.2469566178170.101378109918-0.231883185990.2846483986690.1392264744875.84021392621E-60.629865913010.0673198473713-0.02185345961480.5110297657810.01911541584340.8853166454239.7032550539-48.269500767320.6065649443
31.0416354728-0.1309254498260.2875846804411.1883893572-0.08094556102771.42127147645-0.009688962318410.106952236976-0.209231176471-0.1533160980250.0462459284281-0.009178627798260.2499114533540.02121876237960.002081309423480.2607590810990.01618373117170.02724640699540.300181143887-0.006588080888150.22752394489122.7200665377-13.207692926211.254783912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 186 )A-2 - 1861 - 189
22chain 'A' and (resid 187 through 208 )A187 - 208190 - 298
32chain 'A' and (resid 1001 through 1101 )A1001 - 1101299 - 390
43chain 'A' and (resid 1102 through 1106 )1102 - 1106
53chain 'A' and (resid 219 through 305 )219 - 305

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