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- PDB-5olg: Structure of the A2A-StaR2-bRIL562-ZM241385 complex at 1.86A obta... -

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Basic information

Entry
Database: PDB / ID: 5olg
TitleStructure of the A2A-StaR2-bRIL562-ZM241385 complex at 1.86A obtained from in meso soaking experiments.
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-Protein Coupled Receptor / Adenosine 2a receptor / 7 TM integral membrane protein / thermostabilizing mutations / membrane proteins
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / 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 / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / 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 / response to amphetamine / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / locomotory behavior / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / 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-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / electron transfer activity / periplasmic space / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / dendrite / neuronal cell body / lipid binding / glutamatergic synapse / apoptotic process / heme binding / 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 / 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
CITRIC ACID / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THIOCYANATE ION / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsRucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R. / Marshall, F.H. / Dore, A.S.
Funding support1items
OrganizationGrant numberCountry
European Union115366
CitationJournal: Sci Rep / Year: 2018
Title: Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals.
Authors: Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R.M. / Marshall, F.H. / Dore, A.S.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,27132
Polymers48,0681
Non-polymers8,20331
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric peak on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint26 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.450, 179.393, 139.600
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 / Cytochrome b-562


Mass: 48067.824 Da / Num. of mol.: 1
Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; ...Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 8 types, 119 molecules

#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-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 % / Description: 0.060-0.080 mm long plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol, 0.5 mM theophylline. ZM241385 was subsequently added to motherliquor ...Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol, 0.5 mM theophylline. ZM241385 was subsequently added to motherliquor for the soaking experiment at a final concentration of 0.005 mM.
PH range: 5.3-5.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.53 Å / Num. obs: 42870 / % possible obs: 98.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.7
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.197 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12RC2_2821)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZJ

5mzj


Resolution: 1.87→41.31 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.67
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3894 5 %Random
Rwork0.189 ---
obs0.191 41376 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.73 Å2
Refinement stepCycle: LAST / Resolution: 1.87→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 534 88 3636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123703
X-RAY DIFFRACTIONf_angle_d1.4474946
X-RAY DIFFRACTIONf_dihedral_angle_d16.6172276
X-RAY DIFFRACTIONf_chiral_restr0.07551
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shellResolution: 1.865→1.932 Å
RfactorNum. reflection% reflection
Rfree0.5144 200 -
Rwork0.4834 3701 -
obs--100 %
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)
10.67590.09550.19730.66910.01230.82080.0198-0.0048-0.0381-0.0743-0.0088-0.0320.0917-0.0559-00.1778-0.00240.00310.18590.00640.1615-22.1678-7.056317.6583
20.077-0.0034-0.07210.1943-0.09530.21070.0456-0.26580.3529-0.29420.0507-0.15410.15640.10430.00070.40540.0712-0.01240.3022-0.02610.67490.1168-54.561119.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A'A - 305-1 - A
2X-RAY DIFFRACTION2CHAIN 'A'A - 11061001 - A

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