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- PDB-6aqf: Crystal structure of A2AAR-BRIL in complex with the antagonist ZM... -

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Basic information

Entry
Database: PDB / ID: 6aqf
TitleCrystal structure of A2AAR-BRIL in complex with the antagonist ZM241385 produced from Pichia pastoris
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / A2AAR / GPCR / adenosine receptor / human A2AAR_BRIL chimera / LCP / antagonist complex / Pichia pastoris
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 / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / 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 / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / 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 / dendrite / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / 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
CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsEddy, M.T. / Lee, M.Y. / Gao, Z. / White, K. / Didenko, T. / Horst, R. / Audet, M. / Stanczak, P. / McClary, K.M. / Han, G.W. ...Eddy, M.T. / Lee, M.Y. / Gao, Z. / White, K. / Didenko, T. / Horst, R. / Audet, M. / Stanczak, P. / McClary, K.M. / Han, G.W. / Jacobson, K.A. / Stevens, R.C. / Wuthrich, K.
CitationJournal: Cell / Year: 2018
Title: Allosteric Coupling of Drug Binding and Intracellular Signaling in the A2A Adenosine Receptor.
Authors: Eddy, M.T. / Lee, M.Y. / Gao, Z.G. / White, K.L. / Didenko, T. / Horst, R. / Audet, M. / Stanczak, P. / McClary, K.M. / Han, G.W. / Jacobson, K.A. / Stevens, R.C. / Wuthrich, K.
History
DepositionAug 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 4, 2023Group: 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)53,54617
Polymers48,2891
Non-polymers5,25716
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint25 kcal/mol
Surface area21390 Å2
Unit cell
Length a, b, c (Å)39.837, 180.973, 140.574
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: 48289.180 Da / Num. of mol.: 1
Fragment: UNP P29274 residues 2-208 and 219-316 linked via UNP P0ABE7 residues 23-128,UNP P29274 residues 2-208 and 219-316 linked via UNP P0ABE7 residues 23-128,UNP P29274 residues 2-208 and 219-316 ...Fragment: UNP P29274 residues 2-208 and 219-316 linked via UNP P0ABE7 residues 23-128,UNP P29274 residues 2-208 and 219-316 linked via UNP P0ABE7 residues 23-128,UNP P29274 residues 2-208 and 219-316 linked via UNP P0ABE7 residues 23-128
Mutation: M1007W, H1102I, R1106L,M1007W, H1102I, R1106L,M1007W, H1102I, R1106L
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: Pichia (fungus) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 6 types, 35 molecules

#2: Chemical ChemComp-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol / ZM-241,385


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


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


Mass: 282.461 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 26-28 % (v/v) PEG400 40-60 mM sodium thiocyanate 2% (v/v) 2,5-hexanediol 100mM sodium citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→30.16 Å / Num. obs: 16063 / % possible obs: 90.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 53.72 Å2 / Net I/σ(I): 6.3
Reflection shellHighest resolution: 2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.581 / % possible all: 78.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 2.51→30.16 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.89 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.597 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.585 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.3
RfactorNum. reflection% reflectionSelection details
Rfree0.256 797 4.97 %RANDOM
Rwork0.22 ---
obs0.222 16035 89.4 %-
Displacement parametersBiso mean: 60.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.665 Å20 Å20 Å2
2--0.7979 Å20 Å2
3---0.8671 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.51→30.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 288 19 3257
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013313HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064487HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1550SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes470HARMONIC5
X-RAY DIFFRACTIONt_it3313HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.16
X-RAY DIFFRACTIONt_other_torsion2.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion444SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3714SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.234 106 4.32 %
Rwork0.211 2349 -
all0.212 2455 -
obs--77.4 %
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)
10.8681-0.1586-0.07061.13360.02610.93040.00510.01510.0597-0.0518-0.02140.048-0.08250.02830.0163-0.1732-0.0024-0.0007-0.2452-0.0129-0.265622.2278188.39417.7777
22.7786-2.6997-0.37879.30111.85714.76230.007-0.2175-0.276-0.08320.16640.206-0.02370.0679-0.1734-0.16170.0591-0.0156-0.29670.00240.0962-2.3143236.46620.2439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|-2 - A|306 }
2X-RAY DIFFRACTION2{ A|1001 - A|1106 }

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