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- PDB-8rwh: Dark structure of the human adenosine A2A receptor bound to synth... -

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Basic information

Entry
Database: PDB / ID: 8rwh
TitleDark 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 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 / Surfactant metabolism ...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 / Surfactant metabolism / sensory perception / 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 / prepulse inhibition / cellular defense response / phagocytosis / 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 / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (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: 2.45 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 4, 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)58,29630
Polymers49,8291
Non-polymers8,46729
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint44 kcal/mol
Surface area20370 Å2
MethodPISA
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
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 , 7 types, 57 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.: 22 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 28 / 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 temperature / 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: 2.45→142.13 Å / Num. obs: 20116 / % possible obs: 100 % / Redundancy: 691.8 % / CC1/2: 0.993 / CC star: 0.998 / R split: 0.0776 / Net I/σ(I): 8.89
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 109.1 % / Mean I/σ(I) obs: 0.71 / Num. unique obs: 1902 / CC1/2: 0.278 / CC star: 0.66 / R split: 1.3841 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Description: high viscosity extruder / Injector temperature: 293 K / Jet diameter: 75 µm
Serial crystallography data reductionFrames indexed: 76544

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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: 2.45→45.64 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2000 9.94 %
Rwork0.1913 --
obs0.1958 20116 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 419 28 3349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033512
X-RAY DIFFRACTIONf_angle_d0.5494738
X-RAY DIFFRACTIONf_dihedral_angle_d9.959703
X-RAY DIFFRACTIONf_chiral_restr0.036549
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.40331400.35971270X-RAY DIFFRACTION99
2.51-2.580.39571390.3181256X-RAY DIFFRACTION99
2.58-2.660.32471380.27611250X-RAY DIFFRACTION99
2.66-2.740.31911420.24881288X-RAY DIFFRACTION99
2.74-2.840.31661390.24851261X-RAY DIFFRACTION99
2.84-2.950.23831420.21761280X-RAY DIFFRACTION99
2.95-3.090.23841400.1851273X-RAY DIFFRACTION99
3.09-3.250.25691410.17921277X-RAY DIFFRACTION99
3.25-3.450.24711430.17571299X-RAY DIFFRACTION100
3.45-3.720.19021430.17131294X-RAY DIFFRACTION100
3.72-4.090.20331460.1581320X-RAY DIFFRACTION100
4.09-4.680.20421430.15011298X-RAY DIFFRACTION100
4.69-5.90.23981480.18861339X-RAY DIFFRACTION100
5.9-45.640.24141560.19951411X-RAY DIFFRACTION100

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