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- PDB-6zdv: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 6zdv
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 5d
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsPROTEIN BINDING / G protein-coupled receptor / membrane protein / receptor
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 / electron transport chain / 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 / periplasmic space / electron transfer activity / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / heme binding / 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 / 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 / Chem-QGW / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsVerdon, G. / Jespers, W. / Azuaje, J. / Majellaro, M. / Keranen, H. / Garcia-mera, X. / Congreve, M. / Deflorian, F. / de Graaf, C. / Zhukov, A. ...Verdon, G. / Jespers, W. / Azuaje, J. / Majellaro, M. / Keranen, H. / Garcia-mera, X. / Congreve, M. / Deflorian, F. / de Graaf, C. / Zhukov, A. / Dore, A. / Mason, J. / Aqvist, J. / Cooke, R. / Sotelo, E. / Gutierrez-de-Teran, H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A 2A Adenosine Receptor Antagonists.
Authors: Jespers, W. / Verdon, G. / Azuaje, J. / Majellaro, M. / Keranen, H. / Garcia-Mera, X. / Congreve, M. / Deflorian, F. / de Graaf, C. / Zhukov, A. / Dore, A.S. / Mason, J.S. / Aqvist, J. / ...Authors: Jespers, W. / Verdon, G. / Azuaje, J. / Majellaro, M. / Keranen, H. / Garcia-Mera, X. / Congreve, M. / Deflorian, F. / de Graaf, C. / Zhukov, A. / Dore, A.S. / Mason, J.S. / Aqvist, J. / Cooke, R.M. / Sotelo, E. / Gutierrez-de-Teran, H.
History
DepositionJun 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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)54,20522
Polymers47,9971
Non-polymers6,20821
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint3 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.414, 179.833, 140.085
Angle α, β, γ (deg.)90, 90, 90
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: 47996.746 Da / Num. of mol.: 1
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 , 7 types, 110 molecules

#2: Chemical ChemComp-QGW / [2-methyl-3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl] ethanoate


Mass: 357.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CLR / CHOLESTEROL


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


Mass: 282.461 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O2
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: PEG 400, Sodium Citrate, Sodium Thiocyanate, 2,5 Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→42.808 Å / Num. obs: 25511 / % possible obs: 91.8 % / Redundancy: 9.4 % / CC1/2: 0.998 / Net I/σ(I): 11
Reflection shellResolution: 2.13→2.243 Å / Num. unique obs: 1268 / CC1/2: 0.458

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IU4

5iu4


Resolution: 2.13→42.8 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.248 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.178
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1260 -RANDOM
Rwork0.215 ---
obs0.2155 25511 84 %-
Displacement parametersBiso mean: 49.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.8818 Å20 Å20 Å2
2--5.4951 Å20 Å2
3----3.6133 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.13→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 277 89 3304
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0233309HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.594479HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1199SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3282HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion441SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3059SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion20.16
LS refinement shellResolution: 2.13→2.2 Å
RfactorNum. reflection% reflection
Rfree0.263 27 -
Rwork0.1961 --
obs--11.29 %
Refinement TLS params.

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)
10.13560.0971-0.20040.25050.03030.0821-0-0.0555-0.0355-0.0555-0.01380.0447-0.03550.04470.0139-0.0034-0.006-0.00070.0306-0.0029-0.05322.0383187.030717.8505
20.2998-0.7667-0.07610.5443-0.540500.107-0.5054-0.2474-0.50540.1966-0.0644-0.2474-0.0644-0.3036-0.10150.09250.0346-0.20210.04950.2514-1.8344234.893419.9907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-1 - A|208 A|219 - A|305 A|1201 - A|1201 }A0 - 208
2X-RAY DIFFRACTION1{ A|-1 - A|208 A|219 - A|305 A|1201 - A|1201 }A219 - 305
3X-RAY DIFFRACTION1{ A|-1 - A|208 A|219 - A|305 A|1201 - A|1201 }A1201
4X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

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