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- PDB-3pwh: Thermostabilised Adenosine A2A Receptor -

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Basic information

Entry
Database: PDB / ID: 3pwh
TitleThermostabilised Adenosine A2A Receptor
ComponentsAdenosine receptor A2a
KeywordsSIGNALING PROTEIN / 7TM / GPCR / inverse agonist / 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 / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / intermediate filament / response to caffeine / blood circulation / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / presynaptic active zone / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / prepulse inhibition / cellular defense response / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / positive regulation of apoptotic signaling pathway / central nervous system development / positive regulation of long-term synaptic potentiation / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / positive regulation of protein secretion / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / 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-ZMA / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.296 Å
AuthorsDore, A.S. / Robertson, N. / Errey, J.C. / Ng, I. / Tehan, B. / Hurrell, E. / 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
DepositionDec 8, 2010Deposition 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 20, 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)36,8162
Polymers36,4791
Non-polymers3371
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)111.935, 112.551, 125.678
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 K122A V239A R107A L202A L235A 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-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


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.425463 Å3/Da / Density % sol: 77.329124 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 32-42% PEG1000, 0.25M MgCl2, 0.3% NG, 0.1%(w/v) 1-Butanol, 0.05% CYMAL-6, 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: DECTRIS 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: 3.296→83.844 Å / Num. obs: 12191 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 96.1 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 10.3

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Processing

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

3eml


Resolution: 3.296→19.842 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.54 / σ(F): 1.35 / Phase error: 40.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3156 576 4.8 %Random
Rwork0.2761 11434 --
obs0.2779 12010 98.06 %-
all-12010 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.895 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso max: 430.58 Å2 / Biso mean: 139.5179 Å2 / Biso min: 64.98 Å2
Baniso -1Baniso -2Baniso -3
1--60.7636 Å20 Å20 Å2
2--18.4504 Å2-0 Å2
3---42.3132 Å2
Refinement stepCycle: LAST / Resolution: 3.296→19.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 25 0 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0012338
X-RAY DIFFRACTIONf_angle_d0.3883187
X-RAY DIFFRACTIONf_chiral_restr0.027377
X-RAY DIFFRACTIONf_plane_restr0.002390
X-RAY DIFFRACTIONf_dihedral_angle_d10.444791
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 (%)
3.2962-3.62610.48751340.39712743287795
3.6261-4.14670.29811510.28282820297199
4.1467-5.20870.2681440.22952878302299
5.2087-19.84210.31651470.26382993314099
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)
10.2837-0.0605-0.22521.0271-0.93291.16110.305-1.1647-0.69160.69590.3460.3410.0072-0.50342.5930.9211-0.0079-0.27120.78681.10060.049430.090320.022741.8459
20.01790.01880.00990.01260.01050.00720.24310.44990.35060.4031-0.20150.13790.56530.2159-0.00150.6181-0.3004-0.00021.2560.06742.478911.9521.408829.5774
30.340.1162-0.55550.0304-0.17620.8841-0.00730.9717-0.38670.8159-0.1882-0.03080.04050.7148-0.00030.64440.0104-0.0720.69580.40782.199533.796817.820833.2584
40.0494-0.05920.00140.0616-0.00140.0010.439-0.44430.3581-0.87610.1256-0.0364-0.18940.6682-0.00350.76740.4522-0.03091.4392-0.11613.201152.137.766631.2759
50.9018-0.17480.0520.17280.01810.21850.36030.2035-0.216-0.83780.65620.01350.09-0.94553.72470.94180.05880.11720.65180.73390.307733.134521.910823.7102
60.0855-0.0189-0.11590.05710.02250.133-0.13570.77080.04480.2042-0.78620.867-0.61830.30150.00160.7109-0.0667-0.31361.47490.33342.520113.192427.659714.2698
70.10870.19020.14550.31160.25660.18680.12890.9782-0.2504-1.41470.2723-0.17160.05171.54580.00150.9309-0.0492-0.09561.2932-0.15471.68933.206615.015219.2255
80.0395-0.0348-0.05770.0360.05260.0808-1.16380.8039-0.2811-2.1942-0.51670.41010.2744-0.07320.00271.1242-0.2078-0.08090.76070.01853.056956.601414.315421.3033
90.1730.0423-0.10810.05270.07940.2845-0.25751.2049-0.66240.55180.5917-0.09980.26571.3951-0.00071.01420.18860.07971.3040.03672.654356.112713.613129.0989
100.45780.52120.30650.93020.63360.4198-0.6245-0.81161.30170.8934-0.33530.3319-0.2005-0.1411-0.00410.70170.1718-0.12590.89130.13221.494930.693734.988717.9274
110.0230.00270.01850.12820.21090.3368-0.32291.0170.71520.89950.11960.16710.94091.1865-0.00120.7062-0.0814-0.29211.75840.67762.10992.280646.363419.0215
127.1391-0.6267-3.23331.9193-0.30722.5122-0.11250.75331.9754-0.80690.1149-0.0020.1038-0.5891-0.07030.3774-0.0882-0.03360.1430.00391.228331.721534.256826.8291
135.41417.31052.41892.01083.36811.08830.9678-0.0944-0.49391.5923-0.74720.71350.1913-1.0872-0.1050.39170.2507-0.3550.6275-0.2841.578958.665833.006730.2595
140.21950.2123-0.14580.3633-0.24020.1975-0.1603-0.28711.03020.76560.530.4867-0.7544-0.1844-0.00070.7046-0.09030.00280.6132-0.06451.603634.615229.292337.1347
150.2272-0.0647-0.68920.65471.12323.91041.32920.2356-0.40170.152-1.0581.4699-1.9681-3.0048-0.0150.6927-0.03360.08121.60930.00672.34913.734325.752341.9297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 7:33A7 - 33
2X-RAY DIFFRACTION2chain A and resid 34:40A34 - 40
3X-RAY DIFFRACTION3chain A and resid 41:68A41 - 68
4X-RAY DIFFRACTION4chain A and resid 69:76A69 - 76
5X-RAY DIFFRACTION5chain A and resid 77:104A77 - 104
6X-RAY DIFFRACTION6chain A and resid 105:118A105 - 118
7X-RAY DIFFRACTION7chain A and resid 119:141A119 - 141
8X-RAY DIFFRACTION8chain A and resid 142:151A142 - 151
9X-RAY DIFFRACTION9chain A and resid 158:175A158 - 175
10X-RAY DIFFRACTION10chain A and resid 176:211A176 - 211
11X-RAY DIFFRACTION11chain A and resid 212:220A212 - 220
12X-RAY DIFFRACTION12chain A and resid 221:258A221 - 258
13X-RAY DIFFRACTION13chain A and resid 259:267A259 - 267
14X-RAY DIFFRACTION14chain A and resid 268:292A268 - 292
15X-RAY DIFFRACTION15chain A and resid 293:305A293 - 305

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