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- PDB-6lpk: A2AR crystallized in EROCOC17+4, LCP-SFX at 293 K -

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Basic information

Entry
Database: PDB / ID: 6lpk
TitleA2AR crystallized in EROCOC17+4, LCP-SFX at 293 K
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / LCP crystallization / Isoprenoid-Chained-Lipid / GPCR / SFX
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
Octadecane / CHOLESTEROL / DECANE / DODECANE / Chem-ER0 / HEXANE / PENTADECANE / N-OCTANE / TRIDECANE / UNDECANE ...Octadecane / CHOLESTEROL / DECANE / DODECANE / Chem-ER0 / HEXANE / PENTADECANE / N-OCTANE / TRIDECANE / UNDECANE / 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 / Resolution: 1.8 Å
AuthorsIhara, K. / Hato, M. / Nakane, T. / Yamashita, K. / Kimura-Someya, T. / Hosaka, T. / Ishizuka-Katsura, Y. / Tanaka, R. / Tanaka, T. / Sugahara, M. ...Ihara, K. / Hato, M. / Nakane, T. / Yamashita, K. / Kimura-Someya, T. / Hosaka, T. / Ishizuka-Katsura, Y. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Hirata, K. / Yamamoto, M. / Nureki, O. / Tono, K. / Nango, E. / Iwata, S. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP16K14688 Japan
CitationJournal: Sci Rep / Year: 2020
Title: Isoprenoid-chained lipid EROCOC 17+4 : a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography.
Authors: Ihara, K. / Hato, M. / Nakane, T. / Yamashita, K. / Kimura-Someya, T. / Hosaka, T. / Ishizuka-Katsura, Y. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Hirata, K. / Yamamoto, M. / Nureki, O. / ...Authors: Ihara, K. / Hato, M. / Nakane, T. / Yamashita, K. / Kimura-Someya, T. / Hosaka, T. / Ishizuka-Katsura, Y. / Tanaka, R. / Tanaka, T. / Sugahara, M. / Hirata, K. / Yamamoto, M. / Nureki, O. / Tono, K. / Nango, E. / Iwata, S. / Shirouzu, M.
History
DepositionJan 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 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,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,05728
Polymers49,9741
Non-polymers6,08327
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint23 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.500, 179.200, 142.900
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,Adenosine receptor A2a / Cytochrome b-562


Mass: 49974.281 Da / Num. of mol.: 1 / Mutation: M29W, H124I, R128L
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 , 13 types, 143 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


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#6: Chemical
ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H32
#7: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38
#9: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#10: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18
#11: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24
#12: Chemical ChemComp-ER0 / [(2~{R},3~{S})-2,3,4-tris(oxidanyl)butyl] (5~{R},9~{R},13~{R})-5,9,13,17-tetramethyloctadecanoate


Mass: 444.688 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H52O5 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H28
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate pH5.5, 37% PEG300, 50 mM NaSCN, and 2% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.23 Å
DetectorType: MPCCD / Detector: CCD / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 1.8→30.4 Å / Num. obs: 48924 / % possible obs: 100 % / Redundancy: 306.5 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.995 / R split: 0.071 / Net I/σ(I): 7.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 90.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2438 / CC1/2: 0.393 / R split: 1.079 / % possible all: 100
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EYI

4eyi


Resolution: 1.8→30.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.63 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2453 5 %RANDOM
Rwork0.1769 ---
obs0.1786 46445 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.02 Å2 / Biso mean: 54.105 Å2 / Biso min: 23.65 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.98 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.8→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 431 116 3583
Biso mean--76.62 58.29 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133525
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173797
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6564697
X-RAY DIFFRACTIONr_angle_other_deg1.311.6178806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4445388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06321.644146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34115517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2721517
X-RAY DIFFRACTIONr_chiral_restr0.090.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 177 -
Rwork0.346 3405 -
all-3582 -
obs--100 %

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