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- PDB-5wf5: Agonist bound human A2a adenosine receptor with D52N mutation at ... -

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Basic information

Entry
Database: PDB / ID: 5wf5
TitleAgonist bound human A2a adenosine receptor with D52N mutation at 2.60 A resolution
ComponentsHuman A2a adenosine receptor T4L chimera
KeywordsMEMBRANE PROTEIN / human A2a adenosine receptor / D52N / GPCR-T4L chimera / LCP / agonist / UK432097 / Activation microswitch / allosteric Na-site mutant / GPCR signaling
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 / viral release from host cell by cytolysis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / peptidoglycan catabolic process / 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 / 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 wall macromolecule catabolic process / lysozyme / cell-cell signaling / lysozyme activity / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / host cell cytoplasm / calmodulin binding / defense response to bacterium / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / 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 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Adenosine A2A receptor / Adenosine receptor / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-UKA / Endolysin / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWhite, K.L. / Eddy, M.T. / Gao, Z. / Han, G.W. / Hanson, M.A. / Lian, T. / Deary, A. / Patel, N. / Jacobson, K.A. / Katritch, V. / Stevens, R.C.
CitationJournal: Structure / Year: 2018
Title: Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling.
Authors: White, K.L. / Eddy, M.T. / Gao, Z.G. / Han, G.W. / Lian, T. / Deary, A. / Patel, N. / Jacobson, K.A. / Katritch, V. / Stevens, R.C.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Human A2a adenosine receptor T4L chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0464
Polymers56,5551
Non-polymers1,4913
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.686, 77.769, 86.488
Angle α, β, γ (deg.)90.00, 101.05, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Human A2a adenosine receptor T4L chimera / Lysis protein / Lysozyme / Muramidase


Mass: 56555.074 Da / Num. of mol.: 1 / Mutation: R1012G C1054T C1097A I1137R
Source method: isolated from a genetically manipulated source
Details: D52N mutation
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADORA2A, ADORA2 / Plasmid: pFASTBAC / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P29274, UniProt: P00720, lysozyme
#2: Chemical ChemComp-UKA / 6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide


Mass: 777.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H47N11O6 / Comment: agonist*YM
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 296 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate pH 5, 24-27% (v/v) polyethylene glycol (PEG) 400, 30-80 mM MgCl 2 , 5% (v/v) Jeffamine M-600 pH 7 (Hampton)

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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: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→46.8 Å / Num. obs: 17786 / % possible obs: 92.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.503 / % possible all: 69.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3EML

3eml


Resolution: 2.6→29.909 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.94
RfactorNum. reflection% reflection
Rfree0.2509 907 5.12 %
Rwork0.2138 --
obs0.2158 17709 92.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 83 3 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033647
X-RAY DIFFRACTIONf_angle_d0.4594960
X-RAY DIFFRACTIONf_dihedral_angle_d16.7962177
X-RAY DIFFRACTIONf_chiral_restr0.037578
X-RAY DIFFRACTIONf_plane_restr0.003646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.76290.36331180.30262174X-RAY DIFFRACTION72
2.7629-2.9760.32191340.27782654X-RAY DIFFRACTION87
2.976-3.27520.31351480.25782911X-RAY DIFFRACTION97
3.2752-3.74830.27591670.21823010X-RAY DIFFRACTION99
3.7483-4.71950.24571770.20892992X-RAY DIFFRACTION99
4.7195-29.91050.21761630.1933061X-RAY DIFFRACTION99

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