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- PDB-8a2p: Room-temperature structure of the stabilised A2A-LUAA47070 comple... -

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Basic information

Entry
Database: PDB / ID: 8a2p
TitleRoom-temperature structure of the stabilised A2A-LUAA47070 complex determined by synchrotron serial crystallography
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Adenosine receptor A2a / Soluble cytochrome b562
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 / calmodulin binding / periplasmic space / 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-9Y2 / CHOLESTEROL / OLEIC ACID / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMoraes, I. / Kwan, T.O.C. / Axford, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other government United Kingdom
CitationJournal: J.Appl.Crystallogr. / Year: 2023
Title: A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography.
Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / ...Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Tanaka, T. / Owada, S. / Sugahara, M. / Iwata, S. / Orville, A.M. / Watts, A. / Moraes, I.
History
DepositionJun 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,59610
Polymers46,9301
Non-polymers2,6669
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.437, 181.839, 144.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Cytochrome b-562


Mass: 46929.750 Da / Num. of mol.: 1
Mutation: A54L,T88A,R107A,K122A,L202A,L235A,V239A6,S277A,N154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2, cybC / Plasmid: Bac to Bac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-9Y2 / 4-(3,3-dimethylbutanoylamino)-3,5-bis(fluoranyl)-~{N}-(1,3-thiazol-2-yl)benzamide


Mass: 353.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17F2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


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


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.92 Å3/Da / Density % sol: 57.92 % / Description: plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 4.5
Details: 0.1 M tri-sodium citrate pH 4.5, 0.05 M sodium thiocyanate, 29% (v/v) polyethylene glycol 400, 2% (v/v) 2,5-hexanediol
PH range: 4.0-5.5 / Temp details: constant

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 3.5→90.93 Å / Num. obs: 7126 / % possible obs: 99.6 % / Redundancy: 88.9 % / Biso Wilson estimate: 84.1 Å2 / CC1/2: 0.973 / R split: 0.22 / Net I/σ(I): 13.68
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 36 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 344 / CC1/2: 0.595 / R split: 0.641 / % possible all: 100
Serial crystallography sample deliveryDescription: LCP injector / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Flow rate: 8 µL/min / Injector nozzle: gas / Injector temperature: 293 K / Jet diameter: 50 µm / Preparation: High density crystals
Serial crystallography data reductionFrames indexed: 3618

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
DIALS1.10.1data scaling
PHASERv3.24phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OLV

5olv


Resolution: 3.5→90.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 57.019 / SU ML: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2471 696 9.8 %RANDOM
Rwork0.2012 ---
obs0.2055 6398 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 220.29 Å2 / Biso mean: 118.027 Å2 / Biso min: 61.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---2.08 Å20 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 3.5→90.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 164 12 3162
Biso mean--112.57 80.98 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193246
X-RAY DIFFRACTIONr_angle_refined_deg1.4662.0054421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7025388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.26223.577123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26415504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8951516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212337
X-RAY DIFFRACTIONr_rigid_bond_restr0.75733245
X-RAY DIFFRACTIONr_sphericity_free36.00251
X-RAY DIFFRACTIONr_sphericity_bonded17.79153183
LS refinement shellResolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 45 -
Rwork0.288 469 -
all-514 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -16.851 Å / Origin y: -17.252 Å / Origin z: 18.662 Å
111213212223313233
T0.3765 Å20.0255 Å20.0126 Å2-0.32 Å2-0.0209 Å2--0.3293 Å2
L0.3621 °20.1662 °20.1697 °2-0.2747 °2-0.0176 °2--0.146 °2
S-0.0147 Å °0.0169 Å °-0.0559 Å °-0.0678 Å °0.015 Å °-0.148 Å °0.0806 Å °-0.0409 Å °-0.0002 Å °

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