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

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Basic information

Entry
Database: PDB / ID: 6zdr
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4d
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 / NGF-independant TRKA activation ...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 / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / : / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / synaptic transmission, glutamatergic / central nervous system development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / positive regulation of apoptotic signaling pathway / electron transport chain / 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 / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / heme binding / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / 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 / Chem-QGE / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 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)54,05621
Polymers47,9971
Non-polymers6,06020
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint17 kcal/mol
Surface area20530 Å2
Unit cell
Length a, b, c (Å)39.263, 180.226, 140.001
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 , 6 types, 124 molecules

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


Mass: 343.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17NO4S / 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-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
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: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.918→45.06 Å / Num. obs: 32710 / % possible obs: 90.8 % / Redundancy: 6.9 % / CC1/2: 0.862 / Net I/σ(I): 9.2
Reflection shellResolution: 1.92→2 Å / Num. unique obs: 655 / CC1/2: 0.527

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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: 1.918→45.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 0.178 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 1636 -RANDOM
Rwork0.2077 ---
obs0.2082 32710 84.4 %-
Displacement parametersBiso mean: 47.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.8327 Å20 Å20 Å2
2--5.9351 Å20 Å2
3----4.1024 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.918→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 327 104 3389
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0223391HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.474572HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1260SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes541HARMONIC5
X-RAY DIFFRACTIONt_it3365HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3180SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion19.38
LS refinement shellResolution: 1.92→2 Å
RfactorNum. reflection% reflection
Rfree0.2566 35 -
Rwork0.2334 --
obs0.2346 655 14.71 %
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)
10-0.00650.1390.12260.00720.01320.0025-0.04260.024-0.0426-0.0153-0.06220.024-0.06220.0128-0.0004-0.0086-0.00340.04870.0085-0.0596-21.8684-7.321917.8996
20.8283-1.40390.44631.3806-0.428400.0885-0.50150.4264-0.50150.1669-0.14790.4264-0.1479-0.2554-0.02240.0817-0.001-0.1852-0.04630.17861.1531-55.105720.1162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - A|208 A|219 - A|305 A|1201 - A|1201 }A0 - 208
2X-RAY DIFFRACTION1{ A|0 - A|208 A|219 - A|305 A|1201 - A|1201 }A219 - 305
3X-RAY DIFFRACTION1{ A|0 - A|208 A|219 - A|305 A|1201 - A|1201 }A1201
4X-RAY DIFFRACTION2{ A|1001 - A|1106 }A1001 - 1106

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