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- PDB-6s0l: Structure of the A2A adenosine receptor determined at SwissFEL us... -

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Basic information

Entry
Database: PDB / ID: 6s0l
TitleStructure of the A2A adenosine receptor determined at SwissFEL using native-SAD at 4.57 keV from all available diffraction patterns
ComponentsA2a adenosine receptor
KeywordsSIGNALING PROTEIN / native-SAD / Serial femtosecond crystallography / SFX / SwissFEL / Jungfrau
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / synaptic transmission, cholinergic / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / calmodulin binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / 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 / Chem-ZMA / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / SAD / Resolution: 2.65 Å
AuthorsNass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. ...Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, J.C.
CitationJournal: Iucrj / Year: 2020
Title: Advances in long-wavelength native phasing at X-ray free-electron lasers.
Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / ...Authors: Nass, K. / Cheng, R. / Vera, L. / Mozzanica, A. / Redford, S. / Ozerov, D. / Basu, S. / James, D. / Knopp, G. / Cirelli, C. / Martiel, I. / Casadei, C. / Weinert, T. / Nogly, P. / Skopintsev, P. / Usov, I. / Leonarski, F. / Geng, T. / Rappas, M. / Dore, A.S. / Cooke, R. / Nasrollahi Shirazi, S. / Dworkowski, F. / Sharpe, M. / Olieric, N. / Bacellar, C. / Bohinc, R. / Steinmetz, M.O. / Schertler, G. / Abela, R. / Patthey, L. / Schmitt, B. / Hennig, M. / Standfuss, J. / Wang, M. / Milne, C.J.
History
DepositionJun 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A2a adenosine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,89716
Polymers47,9971
Non-polymers4,90115
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint11 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.340, 180.660, 143.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
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 A2a adenosine receptor


Mass: 47996.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274*PLUS

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Non-polymers , 5 types, 15 molecules

#2: Chemical ChemComp-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


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


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 297 K / Method: lipidic cubic phase
Details: 0.1M sodium citrate pH 5.0, 0.05M sodium thiocyanate, 34% PEG400, 5mM ZM241385, 2% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 2.713 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Aug 12, 2018 / Frequency: 25 / Details: KB
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.713 Å / Relative weight: 1
ReflectionResolution: 2.65→35 Å / Num. obs: 29351 / % possible obs: 100 % / Redundancy: 858 % / Biso Wilson estimate: 117.58 Å2 / Net I/σ(I): 23.29
Reflection shellResolution: 2.65→35 Å / Num. unique obs: 29351 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→34.491 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2203 1471 5.03 %
Rwork0.1974 --
obs0.1987 29238 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→34.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 288 0 3286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113355
X-RAY DIFFRACTIONf_angle_d1.6644525
X-RAY DIFFRACTIONf_dihedral_angle_d11.3561956
X-RAY DIFFRACTIONf_chiral_restr0.253519
X-RAY DIFFRACTIONf_plane_restr0.006537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.73550.64521280.60862453X-RAY DIFFRACTION98
2.7355-2.83320.36991310.3342517X-RAY DIFFRACTION99
2.8332-2.94660.31691320.2352524X-RAY DIFFRACTION100
2.9466-3.08060.30581330.232562X-RAY DIFFRACTION100
3.0806-3.24290.32341310.25012486X-RAY DIFFRACTION100
3.2429-3.4460.24581360.20612555X-RAY DIFFRACTION100
3.446-3.71170.25441400.18932553X-RAY DIFFRACTION100
3.7117-4.08470.20481310.1862527X-RAY DIFFRACTION100
4.0847-4.67450.22721370.17622524X-RAY DIFFRACTION100
4.6745-5.88470.23271330.20572533X-RAY DIFFRACTION100
5.8847-34.49350.16911390.18342533X-RAY DIFFRACTION100

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