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- PDB-5n2r: Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2... -

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Basic information

Entry
Database: PDB / ID: 5n2r
TitleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with PSB36 at 2.8A resolution
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,ADENOSINE RECEPTOR A2A SOLUBLE CYTOCHROME B562 ADENOSINE RECEPTOR A2A,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-PROTEIN-COUPLED RECEPTOR / INTEGRAL THERMOSTABILIZING MUTATIONS
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 / electron transport chain / 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 / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / heme 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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)
Similarity search - Domain/homology
Chem-8JN / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / D(-)-TARTARIC ACID / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsCheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
CitationJournal: Structure / Year: 2017
Title: Structures of Human A1 and A2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity.
Authors: Cheng, R.K.Y. / Segala, E. / Robertson, N. / Deflorian, F. / Dore, A.S. / Errey, J.C. / Fiez-Vandal, C. / Marshall, F.H. / Cooke, R.M.
History
DepositionFeb 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562,ADENOSINE RECEPTOR A2A SOLUBLE CYTOCHROME B562 ADENOSINE RECEPTOR A2A,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42933
Polymers47,9971
Non-polymers9,43232
Water66737
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint70 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.254, 180.739, 140.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562,ADENOSINE RECEPTOR A2A SOLUBLE CYTOCHROME B562 ADENOSINE RECEPTOR A2A,Adenosine receptor A2a / Cytochrome b-562


Mass: 47996.746 Da / Num. of mol.: 1
Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, ...Mutation: A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A,A54L, T88A, R107A, K122A, N154A, L202A, M1007W, L235A, V239A, S277A, G318A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC, ADORA2A / Plasmid: PFAST-BAC / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): TNI PRO / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 7 types, 69 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-8JN / 1-butyl-3-[(~{E})-3-oxidanylprop-1-enyl]-8-[(1~{R},5~{S})-3-tricyclo[3.3.1.0^{3,7}]nonanyl]-7~{H}-purine-2,6-dione


Mass: 384.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N4O3
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical...
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C18H34O2
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.58 Å3/Da / Density % sol: 52.36 % / Description: RECTANGULAR
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 0.1M MES PH 5.5, 0.2M K/NA TARTRATE, 27.5-40% PEG400, 0.5-1% (V/V) (+/-)-2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015 / Details: (DOUBLE) KB MIRROR PAIR
RadiationMonochromator: DOUBLE SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 2.8→90.38 Å / Num. obs: 12834 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.143 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1807 / CC1/2: 0.611 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSJanuary, 2014data reduction
Aimless0.5.17data scaling
PHASERphasing
RefinementResolution: 2.8→38.36 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2285 658 5.14 %
Rwork0.1877 --
obs0.1898 12814 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 498 37 3528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053542
X-RAY DIFFRACTIONf_angle_d0.5014716
X-RAY DIFFRACTIONf_dihedral_angle_d17.2891170
X-RAY DIFFRACTIONf_chiral_restr0.045529
X-RAY DIFFRACTIONf_plane_restr0.004561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.01610.27211250.24232383X-RAY DIFFRACTION100
3.0161-3.31950.31991120.23192394X-RAY DIFFRACTION100
3.3195-3.79950.21891310.19582402X-RAY DIFFRACTION100
3.7995-4.78550.18671370.15252435X-RAY DIFFRACTION100
4.7855-38.36330.23481530.18692542X-RAY DIFFRACTION100
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)
10.20860.0351-0.11850.1448-0.29391.0324-0.04510.0118-0.0246-0.07180.02110.04230.0120.158800.1334-0.0238-0.00270.201-0.01260.138925.8727184.302320.9676
2-0.0984-0.01040.1450.01550.0154-0.1221-0.2153-0.25220.5607-0.13340.0030.23790.14710.3389-0-0.03960.4054-0.2298-0.99050.08610.88681.8606213.885419.8192
30.0132-0.00660.01010.03270.0436-0.0076-0.0058-0.5078-0.0638-0.30290.39410.1232-0.0698-0.102200.73880.2060.34920.30680.00091.602-0.6091238.255622.1585
40.0275-0.10610.04840.09490.20180.3921-0.17560.24870.0803-0.30.3540.3178-0.0428-0.1487-00.3127-0.0379-0.05350.28460.06120.230416.8408193.887611.4668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 1018 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1019 through 1101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1102 through 305 )

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