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- PDB-8rqq: In meso structure of the adenosine A2a G protein-coupled receptor... -

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Basic information

Entry
Database: PDB / ID: 8rqq
TitleIn meso structure of the adenosine A2a G protein-coupled receptor, A2aR, in 7.10 monoacylglycerol
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / G protein-coupled 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 / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsSmithers, L. / Krawinski, P. / Caffrey, M.
Funding support Ireland, 4items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
Science Foundation Ireland22/FFP-A/10278 Ireland
Irish Research CouncilGOIPG/2019/3074 Ireland
Irish Research CouncilGOIPD/2021/40 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2024
Title: 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins.
Authors: Krawinski, P. / Smithers, L. / van Dalsen, L. / Boland, C. / Ostrovitsa, N. / Perez, J. / Caffrey, M.
History
DepositionJan 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,76117
Polymers49,9741
Non-polymers4,78716
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-8 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.690, 180.440, 141.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49974.281 Da / Num. of mol.: 1
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 , 7 types, 52 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


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


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-A1H2K / 7.10 monoacylglycerol (S-form) / [(2S)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1H52 / 7.10 monoacylglycerol (R-form) / [(2R)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30-35.5 %(v/v) PEG400, 50 mM sodium thiocyanate, 100 mM sodium citrate at pH 5, 0.2 %(v/v) 2,5-hexanediol, and 0.025 mM ZM241385

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X CdTe 9M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→47.167 Å / Num. obs: 16601 / % possible obs: 89.5 % / Redundancy: 20.1 % / Biso Wilson estimate: 41.75 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 2.37→2.46 Å / Num. unique obs: 873 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→47.167 Å / SU ML: 0.3103 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 843 5.09 %
Rwork0.2209 15723 -
obs0.2235 16566 77.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.39 Å2
Refinement stepCycle: LAST / Resolution: 2.37→47.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 333 36 3405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373434
X-RAY DIFFRACTIONf_angle_d0.80644619
X-RAY DIFFRACTIONf_chiral_restr0.1682530
X-RAY DIFFRACTIONf_plane_restr0.0157538
X-RAY DIFFRACTIONf_dihedral_angle_d14.4448618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.520.4011220.2909419X-RAY DIFFRACTION12.77
2.52-2.710.30571010.28161754X-RAY DIFFRACTION52.98
2.71-2.980.31541780.27513274X-RAY DIFFRACTION98.63
2.98-3.420.30991630.24883364X-RAY DIFFRACTION99.97
3.42-4.30.26021930.19483372X-RAY DIFFRACTION100
4.3-45.110.25011860.20193540X-RAY DIFFRACTION99.92
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)
10.762412378692-0.2274984687780.03490954020351.824985307010.03213892625720.631419716525-0.0599034696638-0.00996190012816-0.02876937201790.01628235732590.0826271290657-0.130327747146-0.004912583690270.0161813419993-0.01802225544170.2428429435080.0009957938300310.001186520267250.3276145797770.008536532264170.120412883964-21.223452738-9.8864435669120.7845408465
23.69557758888-2.859375191130.7516014725279.15163601061-0.9766326527689.560753647690.248907347369-0.404161376440.285743110704-0.269622135325-0.124059972279-0.1568474682560.09683427217340.106811472127-0.1436553069270.4833332604580.00261440596523-0.04918431177390.54215144507-0.04267748655380.7117311503670.517335664373-57.865418726921.9538387864
30.6013047124730.497296048518-0.09226047002154.023705856350.6195788726560.948268360115-0.1438138751780.0548669472494-0.06436577627760.09360514024950.2094437545530.007030059555090.1187326838250.0381123228541-0.07669920794670.2528623476940.04302799433790.01441504781050.3697625277750.01906266263450.14584830043-17.4071211448-13.440560451611.0976459747
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 208 )A-1 - 208
2X-RAY DIFFRACTION1chain 'A' and (resid 1001 through 1019 )A1001 - 1019
3X-RAY DIFFRACTION2chain 'A' and (resid 1020 through 1101 )A1020 - 1101
4X-RAY DIFFRACTION3chain 'A' and (resid 1102 through 1106 )A1102 - 1106
5X-RAY DIFFRACTION3chain 'A' and (resid 219 through 307 )A219 - 307

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