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- PDB-9fup: Serial microseconds crystallography at ID29 using fixed-target (s... -

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Basic information

Entry
Database: PDB / ID: 9fup
TitleSerial microseconds crystallography at ID29 using fixed-target (small foils): A2a adenosine receptor co-crystallised with Istradefylline
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsSIGNALING PROTEIN / Serial crystallography / serial microsecond crystallography / room temperature / ID29 / ESRF-EBS / fixed-target / foils / membrane protein / A2A receptor / Istradefylline
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 / Chem-JQ9 / 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: 2.5 Å
AuthorsOrlans, J. / Rose, S.L. / Ferguson, G. / Lebon, G. / Basu, S. / de Sanctis, D.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0019 France
CitationJournal: Commun Chem / Year: 2025
Title: Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron.
Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez ...Authors: Orlans, J. / Rose, S.L. / Ferguson, G. / Oscarsson, M. / Homs Puron, A. / Beteva, A. / Debionne, S. / Theveneau, P. / Coquelle, N. / Kieffer, J. / Busca, P. / Sinoir, J. / Armijo, V. / Lopez Marrero, M. / Felisaz, F. / Papp, G. / Gonzalez, H. / Caserotto, H. / Dobias, F. / Gigmes, J. / Lebon, G. / Basu, S. / de Sanctis, D.
History
DepositionJun 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,71621
Polymers46,6151
Non-polymers6,10120
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint14 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.170, 179.400, 142.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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 Adenosine receptor A2a,Soluble cytochrome b562 / Cytochrome b-562


Mass: 46615.297 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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 62 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 11 / 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-JQ9 / 8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione / istradefylline


Mass: 384.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.75 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 0.1 M tri-sodium citrate pH 5.0, 50 mM sodium thiocyanate, 29-30% (v/v) PEG 400, 1% (v/v) 1,6-hexanediol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Sep 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→89.7 Å / Num. obs: 18404 / % possible obs: 100 % / Redundancy: 208 % / Biso Wilson estimate: 63.85 Å2 / CC star: 0.9861 / R split: 0.2311 / Net I/σ(I): 4.33
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 796 / CC star: 0.5244 / R split: 2.4647
Serial crystallography sample deliveryDescription: small foils / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→55.77 Å / SU ML: 0.4316 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.8784
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 1808 10.09 %
Rwork0.2511 16113 -
obs0.2548 17921 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.53 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 347 42 3195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223221
X-RAY DIFFRACTIONf_angle_d0.4684357
X-RAY DIFFRACTIONf_chiral_restr0.0331516
X-RAY DIFFRACTIONf_plane_restr0.0038521
X-RAY DIFFRACTIONf_dihedral_angle_d16.43631330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.570.4261280.3741085X-RAY DIFFRACTION88.8
2.57-2.640.41191290.35281079X-RAY DIFFRACTION85.37
2.64-2.730.34651320.3341185X-RAY DIFFRACTION96.98
2.73-2.830.32121370.33411226X-RAY DIFFRACTION97.36
2.83-2.940.39911380.36581244X-RAY DIFFRACTION99.14
2.94-3.070.35951400.29341262X-RAY DIFFRACTION99.72
3.07-3.230.28861380.28371236X-RAY DIFFRACTION99.78
3.24-3.440.28751410.25881273X-RAY DIFFRACTION99.86
3.44-3.70.31921420.25961279X-RAY DIFFRACTION100
3.7-4.080.2511420.21451273X-RAY DIFFRACTION99.93
4.08-4.670.22961420.19731278X-RAY DIFFRACTION99.93
4.67-5.880.26751460.23431311X-RAY DIFFRACTION100
5.88-55.770.28381530.24061382X-RAY DIFFRACTION99.87

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