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- PDB-8rwi: Steady state structure of the human adenosine A2A receptor bound ... -

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Basic information

Entry
Database: PDB / ID: 8rwi
TitleSteady state structure of the human adenosine A2A receptor bound to synthetic photoswitch 'StilSwitch2' determined by serial synchrotron crystallography
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 / response to caffeine / blood circulation / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / prepulse inhibition / cellular defense response / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / presynaptic modulation of chemical synaptic transmission / astrocyte activation / 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 / positive regulation of protein secretion / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / apoptotic signaling pathway / locomotory behavior / electron transport chain / negative regulation of inflammatory response / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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: 2.8 Å
AuthorsGlover, H. / Weinert, T.
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 5, 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)56,17023
Polymers49,8291
Non-polymers6,34122
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint39 kcal/mol
Surface area19720 Å2
Unit cell
Length a, b, c (Å)40.550, 182.540, 143.660
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
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, 36 molecules

#2: Chemical ChemComp-A1H3I / 8-[(~{E})-2-[3,4-bis(oxidanyl)phenyl]ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione / 1-PHENYLETHANOL


Mass: 356.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N4O4 / 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.: 17 / 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.: 14 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.85
Details: 0.1 M sodium potassium phosphate pH 5.85, 27-30% PEG 500 MME, 0.2 M sodium thiocyanate, 0.4 mM StilSwitch2

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperautre / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→142.13 Å / Num. obs: 14678 / % possible obs: 100 % / Redundancy: 474.5 % / CC1/2: 0.99 / CC star: 0.997 / R split: 0.0995 / Net I/σ(I): 7.23
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 147 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1425 / CC1/2: 0.285 / CC star: 0.666 / R split: 1.4232 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Description: high viscosity extruder / Injector nozzle: 75 / Injector temperature: 293 K
Serial crystallography data reductionFrames indexed: 41705

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHENIX1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.94 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 34.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3172 681 5.01 %
Rwork0.2745 --
obs0.2766 13606 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 339 14 3188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023228
X-RAY DIFFRACTIONf_angle_d0.4064351
X-RAY DIFFRACTIONf_dihedral_angle_d10.782610
X-RAY DIFFRACTIONf_chiral_restr0.033506
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.020.37561340.34312538X-RAY DIFFRACTION100
3.02-3.320.37651340.34052546X-RAY DIFFRACTION100
3.32-3.790.33941340.28732549X-RAY DIFFRACTION100
3.8-4.770.30241360.24362586X-RAY DIFFRACTION100
4.77-19.940.28961430.25872706X-RAY DIFFRACTION100

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