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- PDB-8du3: Crystal structure of A2AAR-StaR2-bRIL in complex with compound 21a -

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Basic information

Entry
Database: PDB / ID: 8du3
TitleCrystal structure of A2AAR-StaR2-bRIL in complex with compound 21a
ComponentsAdenosine receptor A2a, soluble cytochrome b562 chimera,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / GPCR / LCP / Antagonists / Alzheimer / Parkinson
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 / (4M)-6-bromo-4-(furan-2-yl)quinazolin-2-amine / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShiriaeva, A. / Stauch, B. / Han, G.W. / Cherezov, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: High ligand efficiency quinazoline compounds as novel A 2A adenosine receptor antagonists.
Authors: Bolteau, R. / Duroux, R. / Laversin, A. / Vreulz, B. / Shiriaeva, A. / Stauch, B. / Han, G.W. / Cherezov, V. / Renault, N. / Barczyk, A. / Ravez, S. / Coevoet, M. / Melnyk, P. / Liberelle, M. / Yous, S.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 chimera,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,34926
Polymers49,6711
Non-polymers7,67825
Water91951
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint22 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.600, 179.800, 141.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine receptor A2a, soluble cytochrome b562 chimera,Soluble cytochrome b562,Adenosine receptor A2a / Cytochrome b-562


Mass: 49670.883 Da / Num. of mol.: 1
Mutation: A79L, T113A, R132A, K147A, N179A, L227A, M240W, H335I, R339L, L356A, V360A, S398A
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 , 5 types, 76 molecules

#2: Chemical ChemComp-TKO / (4M)-6-bromo-4-(furan-2-yl)quinazolin-2-amine


Mass: 290.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8BrN3O / 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-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#5: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: Sodium Citrate pH 4.5, sodium thiocyanate, PEG 400, 2,4-hexanediol

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Data collection

DiffractionMean temperature: 123 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19347 / % possible obs: 98 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.5
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 856 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 2.5→42.83 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 896 5.03 %
Rwork0.189 16902 -
obs0.1911 17798 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.41 Å2 / Biso mean: 52.9782 Å2 / Biso min: 20.91 Å2
Refinement stepCycle: final / Resolution: 2.5→42.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 431 51 3466
Biso mean--58.19 43.37 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.660.32311250.25092708283397
2.66-2.860.26031470.206927962943100
2.86-3.150.24131580.188727792937100
3.15-3.610.21131590.1882831299099
3.61-4.540.20991530.15962829298299
4.54-42.830.23141540.19622959311398
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)
10.38640.28440.2110.4540.49071.0119-0.0378-0.04840.05640.01680.03910.01410.0452-0.1378-00.2264-0.0134-0.00080.2790.02410.2187-24.1097-5.565621.091
20.1704-0.15830.01460.4856-0.11660.41690.1268-0.17690.4208-0.27460.0516-0.0045-0.2581-0.03440.3050.48320.0919-0.02630.3772-0.02050.85740.5139-54.697420.0043
30.308-0.08750.27990.1209-0.21350.7113-0.0060.03440.0081-0.33490.0145-0.13870.04750.05220.00010.291-0.00060.03320.2532-0.01280.232-18.0304-10.61911.0892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 208)A0 - 208
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 306)A219 - 306

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