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

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Basic information

Entry
Database: PDB / ID: 8rwc
TitleCrystal structure of the adenosine A2A receptor in complex with the synthetic photoswitch 'StilSwitch2
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 circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / vasodilation / 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 / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / heme binding / dendrite / 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 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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)59,26132
Polymers49,8291
Non-polymers9,43231
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint30 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.424, 179.269, 139.750
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 , 6 types, 105 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.: 4 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: 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: 2.48 Å3/Da / Density % sol: 50.36 % / Description: square plates
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: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→46.58 Å / Num. obs: 22234 / % possible obs: 99.7 % / Redundancy: 38.6 % / CC1/2: 0.997 / Rpim(I) all: 0.044 / Net I/σ(I): 13.9
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2066 / CC1/2: 0.463 / Rpim(I) all: 0.651 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→42.68 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1118 5.04 %
Rwork0.1928 --
obs0.1952 22199 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 507 74 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023467
X-RAY DIFFRACTIONf_angle_d0.5694641
X-RAY DIFFRACTIONf_dihedral_angle_d15.003720
X-RAY DIFFRACTIONf_chiral_restr0.035530
X-RAY DIFFRACTIONf_plane_restr0.003555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.420.35291250.27882534X-RAY DIFFRACTION98
2.42-2.540.29721300.24412584X-RAY DIFFRACTION99
2.54-2.70.25061370.1942610X-RAY DIFFRACTION100
2.7-2.910.24741500.19012601X-RAY DIFFRACTION100
2.91-3.210.23841690.18742601X-RAY DIFFRACTION100
3.21-3.670.23571330.18152660X-RAY DIFFRACTION100
3.67-4.620.22391250.16462683X-RAY DIFFRACTION100
4.62-42.680.21771490.19572808X-RAY DIFFRACTION100

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