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- PDB-3rey: Thermostabilised adenosine A2A receptor in complex with XAC -

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Basic information

Entry
Database: PDB / ID: 3rey
TitleThermostabilised adenosine A2A receptor in complex with XAC
ComponentsAdenosine receptor A2a
KeywordsSIGNALING PROTEIN / 7TM / GPCR / G-PROTEIN / MEMBRANE PROTEIN
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 / presynaptic modulation of chemical synaptic transmission / 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 / blood coagulation / vasodilation / 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 / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / 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 / 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) ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-XAC / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.309 Å
AuthorsDore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. ...Dore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. / Tate, C.G. / Weir, M. / Marshall, F.H.
CitationJournal: Structure / Year: 2011
Title: Structure of the adenosine A(2A) receptor in complex with ZM241385 and the xanthines XAC and caffeine
Authors: Dore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Hollenstein, K. / Tehan, B. / Hurrell, E. / Bennett, K. / Congreve, M. / Magnani, F. / Tate, C.G. / Weir, M. / Marshall, F.H.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 1, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9082
Polymers36,4791
Non-polymers4281
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.865, 113.061, 126.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Adenosine receptor A2a


Mass: 36479.102 Da / Num. of mol.: 1 / Fragment: residues 1-317
Mutation: A54L, T88A, R107A, K122A, L202A, L235A, V239A, S277A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274
#2: Chemical ChemComp-XAC / N-(2-aminoethyl)-2-[4-(2,6-dioxo-1,3-dipropyl-2,3,6,7-tetrahydro-1H-purin-8-yl)phenoxy]acetamide


Mass: 428.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N6O4
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: 5.495351 Å3/Da / Density % sol: 77.617447 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 32-42% PEG1000, 0.25M MGCL2, 0.3% NG, 0.1%(W/V) 1-BUTANOL, 0.05% CYMAL-6, 0.1M TRIS-HCL(PH 8.1), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9777 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 6, 2010
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 3.3→48.69 Å / Num. obs: 10627 / % possible obs: 89.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 5.3 % / Biso Wilson estimate: 101.2 Å2
Reflection shellResolution: 3.3→3.48 Å / % possible all: 90.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_84)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWH

3pwh


Resolution: 3.309→19.938 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.45 / σ(F): 1.35 / Phase error: 42.02 / Stereochemistry target values: ML / Details: SIMULATED ANNEALING, TLS, RESTRAINED REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.3193 491 4.72 %RANDOM
Rwork0.2989 ---
obs0.2999 10404 84.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.287 Å2 / ksol: 0.223 e/Å3
Displacement parametersBiso max: 366.2 Å2 / Biso mean: 156.8514 Å2 / Biso min: 93.93 Å2
Baniso -1Baniso -2Baniso -3
1--78.991 Å20 Å20 Å2
2--16.2441 Å2-0 Å2
3---62.747 Å2
Refinement stepCycle: LAST / Resolution: 3.309→19.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 31 0 2281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012343
X-RAY DIFFRACTIONf_angle_d0.3943193
X-RAY DIFFRACTIONf_chiral_restr0.028377
X-RAY DIFFRACTIONf_plane_restr0.032392
X-RAY DIFFRACTIONf_dihedral_angle_d10.402811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3091-3.64030.44951060.43292185229176
3.6403-4.16290.3661340.34552567270190
4.1629-5.22910.30671340.24822542267687
5.2291-19.93870.28111170.28372619273686
Refinement TLS params.Method: refined / Origin x: 31.9487 Å / Origin y: 25.5491 Å / Origin z: 28.2055 Å
111213212223313233
T0.9335 Å20.006 Å2-0.0567 Å2-1.009 Å2-0.1191 Å2--1.192 Å2
L2.2274 °21.4046 °2-0.3168 °2-3.0223 °2-0.6691 °2--0.9435 °2
S0.1845 Å °0.3374 Å °0.1892 Å °-0.2261 Å °0.0525 Å °0.1308 Å °0.1362 Å °-0.0524 Å °0 Å °
Refinement TLS groupSelection details: chain A

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