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- PDB-3qak: Agonist bound structure of the human adenosine A2a receptor -

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Basic information

Entry
Database: PDB / ID: 3qak
TitleAgonist bound structure of the human adenosine A2a receptor
ComponentsAdenosine receptor A2a,lysozyme chimera
KeywordsSIGNALING PROTEIN / HYDROLASE / Structural Genomics / Protein Structure Initiative / JOINT CENTER FOR INNOVATIVE MEMBRANE PROTEIN TECHNOLOGIES / JCIMPT / Membrane protein / receptor / GPCR Network / GPCR / PSI-Biology
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / viral release from host cell by cytolysis / presynaptic modulation of chemical synaptic transmission / peptidoglycan catabolic process / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cell wall macromolecule catabolic process / blood coagulation / vasodilation / lysozyme / lysozyme activity / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / host cell cytoplasm / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / defense response to bacterium / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-UKA / Endolysin / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo Sapien (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsXu, F. / Wu, H. / Katritch, V. / Han, G.W. / Cherezov, V. / Stevens, R. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2011
Title: Structure of an agonist-bound human A2A adenosine receptor.
Authors: Xu, F. / Wu, H. / Katritch, V. / Han, G.W. / Jacobson, K.A. / Gao, Z.G. / Cherezov, V. / Stevens, R.C.
History
DepositionJan 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Oct 10, 2012Group: Database references
Revision 1.4Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.6Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a,lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2314
Polymers54,7401
Non-polymers1,4913
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.836, 78.944, 86.579
Angle α, β, γ (deg.)90.00, 100.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosine receptor A2a,lysozyme chimera / Endolysin / Lysis protein / Muramidase


Mass: 54739.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapien (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADORA2, ADORA2A, E / Production host: Spodoptera frugiperda (fall armyworm) / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 17

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: PEG400 30%v/v, MgCl2 200mM, pH 5.0, Lipidic cubic phase, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.71→29.61 Å / Num. obs: 16713 / % possible obs: 98 % / Observed criterion σ(F): 1.2 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 1.8 / % possible all: 91.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→29.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.59 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.937 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27308 840 5.1 %RANDOM
Rwork0.21708 ---
obs0.21993 15770 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.68 Å2
2--4.24 Å20 Å2
3----4.31 Å2
Refinement stepCycle: LAST / Resolution: 2.71→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 82 6 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223645
X-RAY DIFFRACTIONr_bond_other_d0.0010.022439
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9724951
X-RAY DIFFRACTIONr_angle_other_deg0.88435914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36422.448143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.95615594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381526
X-RAY DIFFRACTIONr_chiral_restr0.0680.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02799
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.52203
X-RAY DIFFRACTIONr_mcbond_other0.0671.5902
X-RAY DIFFRACTIONr_mcangle_it0.85423554
X-RAY DIFFRACTIONr_scbond_it1.27731442
X-RAY DIFFRACTIONr_scangle_it2.1744.51397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.714→2.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 51 -
Rwork0.389 878 -
obs--74.56 %
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)
11.2176-0.48910.22812.3079-2.78933.4949-0.04270.0729-0.0331-0.0637-0.1183-0.1280.080.1140.1610.1222-0.00770.04050.0632-0.04120.1231-4.7922-8.837237.9701
27.4662-0.11411.02711.5995-0.2623.77290.05440.34380.0303-0.2343-0.0474-0.1660.1054-0.0061-0.0070.06870.01320.0570.04760.02770.0596-0.924615.2730.4406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 308
2X-RAY DIFFRACTION2A1002 - 1161

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