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- PDB-5olo: Structure of the A2A-StaR2-bRIL562-Tozadenant complex at 3.1A obt... -

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Basic information

Entry
Database: PDB / ID: 5olo
TitleStructure of the A2A-StaR2-bRIL562-Tozadenant complex at 3.1A obtained from in meso soaking experiments.
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-Protein Coupled Receptor / Adenosine 2a receptor / 7 TM integral membrane protein / thermostabilizing mutations
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 / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / synaptic transmission, cholinergic / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / response to inorganic substance / cellular defense response / prepulse inhibition / phagocytosis / positive regulation of apoptotic signaling pathway / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / electron transport chain / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / positive regulation of synaptic transmission, GABAergic / apoptotic signaling pathway / positive regulation of protein secretion / 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 / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / apoptotic process / dendrite / lipid binding / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / 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
Chem-9XW / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R. / Marshall, F.H. / Dore, A.S.
Funding support1items
OrganizationGrant numberCountry
European Union115366
CitationJournal: Sci Rep / Year: 2018
Title: Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals.
Authors: Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R.M. / Marshall, F.H. / Dore, A.S.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,33424
Polymers48,0681
Non-polymers7,26623
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric peak from size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint17 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.383, 181.013, 141.774
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,Adenosine receptor A2a / Cytochrome b-562


Mass: 48067.824 Da / Num. of mol.: 1
Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 27 molecules

#2: Chemical ChemComp-9XW / ~{N}-(4-methoxy-7-morpholin-4-yl-1,3-benzothiazol-2-yl)-4-methyl-4-oxidanyl-piperidine-1-carboxamide


Mass: 406.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O4S
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Tozadenant was added to the mother liquor to a ...Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol and 0.5 mM theophylline Tozadenant was added to the mother liquor to a concentration of 0.005 mM for the soaking experiments.
PH range: 5.3-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.1→38.48 Å / Num. obs: 9667 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.078 / Net I/σ(I): 8.3
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.246 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12RC2_2821)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZJ

5mzj


Resolution: 3.1→38.48 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 27.21
RfactorNum. reflection% reflection
Rfree0.245 1782 10.04 %
Rwork0.199 --
obs0.204 9645 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 421 4 3388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023467
X-RAY DIFFRACTIONf_angle_d0.7334644
X-RAY DIFFRACTIONf_dihedral_angle_d11.0492117
X-RAY DIFFRACTIONf_chiral_restr0.042529
X-RAY DIFFRACTIONf_plane_restr0.003553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.18390.40681460.34741228X-RAY DIFFRACTION100
3.1839-3.27760.38131260.30671262X-RAY DIFFRACTION100
3.2776-3.38330.29461470.26421183X-RAY DIFFRACTION100
3.3833-3.50410.26141260.23811246X-RAY DIFFRACTION100
3.5041-3.64430.29161680.21951195X-RAY DIFFRACTION100
3.6443-3.81010.28141070.19781251X-RAY DIFFRACTION100
3.8101-4.01070.24591790.1951194X-RAY DIFFRACTION100
4.0107-4.26170.2301900.17191281X-RAY DIFFRACTION100
4.2617-4.59030.20321810.1651183X-RAY DIFFRACTION100
4.5903-5.05130.2412910.16741272X-RAY DIFFRACTION100
5.0513-5.78010.25491740.19051199X-RAY DIFFRACTION100
5.7801-7.27430.2854830.22381262X-RAY DIFFRACTION100
7.2743-38.48570.18291640.1671213X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.97070.1016-0.51591.6863-0.04282.1667-0.07560.05910.0452-0.00770.07010.0631-0.0050.1394-0.00020.1696-0.0213-0.0580.3013-0.03130.247622.2673187.047818.5918
20.12880.00250.080.0835-0.01910.21220.0719-0.66970.3229-0.70220.10830.6021-0.11420.2342-0.00011.09810.02540.02180.79110.06411.5729-1.7765235.591920.4618
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND (RESSEQ -1:208 OR RESSEQ 219:305 OR RESSEQ 1201))
2X-RAY DIFFRACTION2(CHAIN A AND (RESSEQ 1001:1106))

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