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- PDB-3eml: The 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bou... -

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Basic information

Entry
Database: PDB / ID: 3eml
TitleThe 2.6 A Crystal Structure of a Human A2A Adenosine Receptor bound to ZM241385.
ComponentsHuman Adenosine A2A receptor/T4 lysozyme chimera
KeywordsMEMBRANE PROTEIN / RECEPTOR / adenosine / caffeine / GPCR / LCP / mesophase / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D / GPCR Network
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / 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 / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / 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 / viral release from host cell by cytolysis / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / peptidoglycan catabolic process / neuron projection morphogenesis / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / apoptotic signaling pathway / astrocyte activation / 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 wall macromolecule catabolic process / cell-cell signaling / presynaptic membrane / lysozyme / lysozyme activity / 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 / dendrite / lipid binding / glutamatergic synapse / apoptotic process / 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 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / 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 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
STEARIC ACID / Chem-ZMA / 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
AuthorsJaakola, V.-P. / Griffith, M.T. / Hanson, M.A. / Cherezov, V. / Chien, E.Y.T. / Lane, J.R. / Ijzerman, A.P. / Stevens, R.C. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) / GPCR Network (GPCR)
CitationJournal: Science / Year: 2008
Title: The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist.
Authors: Jaakola, V.P. / Griffith, M.T. / Hanson, M.A. / Cherezov, V. / Chien, E.Y. / Lane, J.R. / Ijzerman, A.P. / Stevens, R.C.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 8, 2012Group: Other
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Human Adenosine A2A receptor/T4 lysozyme chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17214
Polymers54,7401
Non-polymers2,43213
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.736, 76.932, 86.553
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Human Adenosine A2A receptor/T4 lysozyme chimera


Mass: 54739.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Plasmid: pBac5b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P00720
#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 / Comment: antagonist*YM
#3: Chemical
ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H36O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 13

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.79 %
Description: THIS STRUCTURE IS A PART OF THE ROADMAP/PSI COMMUNITY OUTREACH PROGRAM, NOT A SPECIFIC PSI TARGET.
Crystal growTemperature: 293 K / pH: 6.5
Details: PEG400 30%v/v, LiSO4 185mM, NaCitrate 100mM, pH 6.5, Lipidic mesophase, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2008 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 18465 / % possible obs: 96.8 % / Redundancy: 3.4 % / Rsym value: 0.098 / Net I/σ(I): 7.35
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.398 / % possible all: 93.9

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Processing

Software
NameVersionClassification
Blu-IceAPSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RH1

2rh1


Resolution: 2.6→19.42 Å / SU ML: 0.43 / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 937 5.08 %
Rwork0.196 --
obs0.198 18461 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.49 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 160 76 3757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73670.30541400.26232411X-RAY DIFFRACTION94
2.7367-2.90770.28161200.2492472X-RAY DIFFRACTION96
2.9077-3.13130.31271430.23232510X-RAY DIFFRACTION98
3.1313-3.44480.23291450.21662477X-RAY DIFFRACTION97
3.4448-3.93970.1951420.17942533X-RAY DIFFRACTION98
3.9397-4.950.2071200.17382526X-RAY DIFFRACTION98
4.95-19.42110.2181270.18092595X-RAY DIFFRACTION98

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