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- PDB-8jwz: Crystal structure of A2AR-T4L in complex with AB928 -

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Basic information

Entry
Database: PDB / ID: 8jwz
TitleCrystal structure of A2AR-T4L in complex with AB928
ComponentsAdenosine receptor A2a,Endolysin
KeywordsSIGNALING PROTEIN / adenosine receptor / inhibitor / complex
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 / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx ...Adenosine A2A receptor / Adenosine receptor / 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) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Chem-U30 / Endolysin / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsWeng, Y. / Chen, Y. / Xu, Y. / Song, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171215 China
CitationJournal: Sci China Life Sci / Year: 2024
Title: Structural insight into the dual-antagonistic mechanism of AB928 on adenosine A 2 receptors.
Authors: Weng, Y. / Yang, X. / Zhang, Q. / Chen, Y. / Xu, Y. / Zhu, C. / Xie, Q. / Wang, Y. / Yang, H. / Liu, M. / Lu, W. / Song, G.
History
DepositionJun 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,79925
Polymers54,0591
Non-polymers6,74024
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.870, 76.200, 85.660
Angle α, β, γ (deg.)90.000, 101.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 54058.957 Da / Num. of mol.: 1 / Mutation: C54T,C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ADORA2A, ADORA2, e, T4Tp126 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: D9IEF7, lysozyme

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Non-polymers , 7 types, 276 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Chemical ChemComp-U30 / 3-[2-azanyl-6-[1-[[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]methyl]-1,2,3-triazol-4-yl]pyrimidin-4-yl]-2-methyl-benzenecarbonitrile


Mass: 426.474 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H22N8O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 6.6
Details: 100 mM sodium cacodylate trihydrate pH 6.6, 120 mM ammonium tartrate dibasic, 32% PEG 40

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Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→45.9 Å / Num. obs: 24124 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 28.16 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.25
Reflection shellResolution: 2.37→2.51 Å / Redundancy: 15 % / Mean I/σ(I) obs: 1.57 / Num. unique obs: 376 / CC1/2: 0.56 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot1.20.1_4487model building
PHENIX1.20.1_4487refinement
Coot1.20.1_4487model building
Coot1.20.1_4487model building
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→20 Å / SU ML: 0.2933 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5331
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 2001 8.32 %
Rwork0.1889 22051 -
obs0.1933 24052 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.55 Å2
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 421 252 4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023999
X-RAY DIFFRACTIONf_angle_d0.58145325
X-RAY DIFFRACTIONf_chiral_restr0.0939585
X-RAY DIFFRACTIONf_plane_restr0.0032633
X-RAY DIFFRACTIONf_dihedral_angle_d16.6715780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.430.33011550.27471531X-RAY DIFFRACTION99.59
2.43-2.490.29621350.25271581X-RAY DIFFRACTION100
2.49-2.570.30161270.2331577X-RAY DIFFRACTION99.94
2.57-2.650.31531560.21261560X-RAY DIFFRACTION100
2.65-2.750.24671370.21361562X-RAY DIFFRACTION100
2.75-2.850.29681420.20411573X-RAY DIFFRACTION100
2.86-2.980.26721470.19621574X-RAY DIFFRACTION100
2.98-3.140.25881460.20191558X-RAY DIFFRACTION100
3.14-3.340.26481460.19551594X-RAY DIFFRACTION100
3.34-3.590.22911370.17711578X-RAY DIFFRACTION100
3.59-3.950.19441450.16541568X-RAY DIFFRACTION99.94
3.95-4.520.20361360.15071588X-RAY DIFFRACTION100
4.52-5.670.17761440.17171591X-RAY DIFFRACTION99.94
5.67-200.24721480.17921616X-RAY DIFFRACTION99.83

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