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- PDB-8rw4: Crystal structure of the adenosine A2A receptor in complex with t... -

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Basic information

Entry
Database: PDB / ID: 8rw4
TitleCrystal structure of the adenosine A2A receptor in complex with the synthetic photoswitch 'AzoSwitch2
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / adenosine receptor / synthetic photoswitch / Parkinson's disease
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
: / CHOLESTEROL / OLEIC ACID / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGlover, H.
Funding support Switzerland, Germany, 7items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science FoundationCRSII4_213507 Switzerland
Other government42711.1 IP-LS Switzerland
Swiss Nanoscience Institute#1904 Switzerland
German Research Foundation (DFG)1850/4-3 Germany
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography.
Authors: Glover, H. / Sassmannshausen, T. / Bertrand, Q. / Trabuco, M. / Slavov, C. / Bacchin, A. / Andres, F. / Kondo, Y. / Stipp, R. / Wranik, M. / Khusainov, G. / Carrillo, M. / Kekilli, D. / Nan, ...Authors: Glover, H. / Sassmannshausen, T. / Bertrand, Q. / Trabuco, M. / Slavov, C. / Bacchin, A. / Andres, F. / Kondo, Y. / Stipp, R. / Wranik, M. / Khusainov, G. / Carrillo, M. / Kekilli, D. / Nan, J. / Gonzalez, A. / Cheng, R. / Neidhart, W. / Weinert, T. / Leonarski, F. / Dworkowski, F. / Kepa, M. / Wachtveitl, J. / Hennig, M. / Standfuss, J.
History
DepositionFeb 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,75125
Polymers49,8291
Non-polymers6,92224
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint60 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.494, 179.587, 139.991
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 / Cytochrome b-562


Mass: 49829.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-A1H3L / 8-[(~{E})-(3,4-dimethoxyphenyl)diazenyl]-1,3-diethyl-7~{H}-purine-2,6-dione / ASPARTATE SEMIALDEHYDE


Mass: 372.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M Sodium citrate pH 5, 0.05 M Sodium thiocyanate, 3% (v/v) 2-methyl-2,4-pentanediol, 32% (v/v) PEG 400, 1 mM Theophylline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46.66 Å / Num. obs: 25908 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rpim(I) all: 0.091 / Net I/σ(I): 6.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2169 / CC1/2: 0.388 / Rpim(I) all: 0.704 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.41 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1999 7.87 %
Rwork0.1998 --
obs0.2026 25385 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→41.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 357 74 3373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043471
X-RAY DIFFRACTIONf_angle_d0.764687
X-RAY DIFFRACTIONf_dihedral_angle_d17.08661
X-RAY DIFFRACTIONf_chiral_restr0.046540
X-RAY DIFFRACTIONf_plane_restr0.004582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.27051280.24021497X-RAY DIFFRACTION91
2.26-2.320.26031300.23681519X-RAY DIFFRACTION90
2.32-2.380.24721330.20931560X-RAY DIFFRACTION93
2.38-2.460.27941430.21451673X-RAY DIFFRACTION99
2.46-2.550.25241420.20421652X-RAY DIFFRACTION99
2.55-2.650.2371450.2081697X-RAY DIFFRACTION100
2.65-2.770.26131430.20271677X-RAY DIFFRACTION100
2.77-2.920.21981440.19981686X-RAY DIFFRACTION100
2.92-3.10.25231470.19551711X-RAY DIFFRACTION100
3.1-3.340.24421450.20441706X-RAY DIFFRACTION100
3.34-3.680.24161460.18811705X-RAY DIFFRACTION100
3.68-4.210.22231470.1831717X-RAY DIFFRACTION100
4.21-5.30.21251490.18951739X-RAY DIFFRACTION100
5.3-41.410.21551570.20841847X-RAY DIFFRACTION100

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