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- PDB-5olh: Structure of the A2A-StaR2-bRIL562-Vipadenant complex at 2.6A obt... -

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Basic information

Entry
Database: PDB / ID: 5olh
TitleStructure of the A2A-StaR2-bRIL562-Vipadenant complex at 2.6A 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
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / 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 / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / 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 / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / astrocyte activation / presynaptic modulation of chemical synaptic transmission / response to amphetamine / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of mitochondrial membrane potential / positive regulation of protein secretion / excitatory postsynaptic potential / synaptic transmission, glutamatergic / locomotory behavior / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / 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 / calmodulin binding / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / heme binding / dendrite / lipid binding / 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-9XT / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.1Jan 17, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)56,66129
Polymers48,0681
Non-polymers8,59428
Water52229
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 area8630 Å2
ΔGint19 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.400, 179.334, 141.145
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,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,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 , 6 types, 57 molecules

#2: Chemical ChemComp-9XT / 3-[(4-azanyl-3-methyl-phenyl)methyl]-7-(furan-2-yl)-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine


Mass: 321.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#6: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.59 Å3/Da / Density % sol: 52.57 %
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 and 0.5 mM theophylline Vipadenant was added to the mother liquor to a ...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 and 0.5 mM theophylline Vipadenant was added to the mother liquor to a concentration of 0.005 mM for the soaking experiments.
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: Apr 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.82 Å / Num. obs: 15853 / % possible obs: 99.5 % / Redundancy: 8.3 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.248 / Net I/σ(I): 8.3
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.8 / % possible all: 98.7

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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: 2.6→29.82 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.249 1503 5.17 %
Rwork0.2 --
obs0.203 29093 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 482 29 3525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033591
X-RAY DIFFRACTIONf_angle_d0.7394778
X-RAY DIFFRACTIONf_dihedral_angle_d12.9552206
X-RAY DIFFRACTIONf_chiral_restr0.042528
X-RAY DIFFRACTIONf_plane_restr0.003560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6004-2.68430.27221350.26232457X-RAY DIFFRACTION96
2.6843-2.78010.3241450.26732474X-RAY DIFFRACTION97
2.7801-2.89130.30311400.24582532X-RAY DIFFRACTION99
2.8913-3.02280.23991100.23552562X-RAY DIFFRACTION99
3.0228-3.1820.35621520.24822518X-RAY DIFFRACTION99
3.182-3.38110.24841170.20882514X-RAY DIFFRACTION98
3.3811-3.64180.21331560.18972481X-RAY DIFFRACTION98
3.6418-4.00750.20971340.17482486X-RAY DIFFRACTION96
4.0075-4.58560.19851330.16612491X-RAY DIFFRACTION98
4.5856-5.77050.28851460.17842529X-RAY DIFFRACTION99
5.7705-29.81880.21671350.17322546X-RAY DIFFRACTION99
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)
10.87810.0860.18221.75770.06251.30790.0047-0.0015-0.0576-0.0948-0.0045-0.03320.1201-0.0777-0.00010.149-0.01040.01070.21430.02030.123-22.4758-6.028618.104
20.6145-0.0819-0.29992.6109-0.30852.29250.1366-0.13120.4454-0.34720.149-0.1381-0.05070.1765-0.27210.51930.0766-0.00710.4042-0.04120.83190.0233-54.051320.1672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and (resseq -1:208 or resseq 219:305 or resseq 1201))
2X-RAY DIFFRACTION2(chain A and (resseq 1001:1106))

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