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- PDB-6wqa: 2.0A angstrom A2a adenosine receptor structure using XFEL data co... -

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Basic information

Entry
Database: PDB / ID: 6wqa
Title2.0A angstrom A2a adenosine receptor structure using XFEL data collected in helium atmosphere.
ComponentsAdenosine receptor A2a/Soluble cytochrome b562 chimera
KeywordsMEMBRANE PROTEIN / Adenosine A2A receptor / XFEL / Lipidic cubic phase / helium atmosphere
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 / NGF-independant TRKA activation ...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 / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / : / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / synaptic transmission, glutamatergic / central nervous system development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / positive regulation of apoptotic signaling pathway / electron transport chain / 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 / periplasmic space / electron transfer activity / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / heme binding / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / 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
CHOLESTEROL / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLee, M.-Y. / Geiger, J. / Ishchenko, A. / Han, G.W. / Barty, A. / White, T.A. / Gati, C. / Batyuk, A. / Hunter, M.S. / Aquila, A. ...Lee, M.-Y. / Geiger, J. / Ishchenko, A. / Han, G.W. / Barty, A. / White, T.A. / Gati, C. / Batyuk, A. / Hunter, M.S. / Aquila, A. / Boutet, S. / Weierstall, U. / Cherezov, V. / Liu, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM127086 United States
CitationJournal: Iucrj / Year: 2020
Title: Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase
Authors: Lee, M.-Y. / Geiger, J. / Ishchenko, A. / Han, G.W. / Barty, A. / White, T.A. / Gati, C. / Batyuk, A. / Hunter, M.S. / Aquila, A. / Boutet, S. / Weierstall, U. / Cherezov, V. / Liu, W.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,96328
Polymers49,9741
Non-polymers7,98927
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.350, 180.500, 142.700
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 chimera / Cytochrome b-562


Mass: 49974.281 Da / Num. of mol.: 1
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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 8 types, 111 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: 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
#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.: 15 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: PEG400, sodium thiocyanate, sodium citrate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.283 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Dec 15, 2014 / Frequency: 10
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 2→27.7 Å / Num. obs: 35870 / % possible obs: 100 % / Redundancy: 205 % / Biso Wilson estimate: 33.85 Å2 / CC star: 0.99 / R split: 0.19 / Net I/σ(I): 4.1
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 3486 / CC star: 0.5 / R split: 2.11 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionInjector temperature: 293 K
Serial crystallography data reductionCrystal hits: 26341 / Frames indexed: 16737

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PHASER1.17phasing
PDB_EXTRACT3.25data extraction
CrystFEL0.8.0+049c3eb4data reduction
CrystFEL0.8.0+049c3eb4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K2D

5k2d


Resolution: 2→27.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2000 5.58 %RANDOM
Rwork0.193 ---
obs0.194 35862 100 %-
Displacement parametersBiso max: 142.69 Å2 / Biso mean: 49.05 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--2.1385 Å20 Å20 Å2
2--1.1739 Å20 Å2
3---0.9645 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: final / Resolution: 2→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 438 84 3451
Biso mean--63.41 44.72 -
Num. residues----391
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1640SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes499HARMONIC5
X-RAY DIFFRACTIONt_it3457HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion452SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3783SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3457HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4653HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion2.94
LS refinement shellResolution: 2→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.245 160 5.57 %
Rwork0.24 2715 -
all0.24 2875 -
obs--100 %

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