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- PDB-6lpl: A2AR crystallized in EROCOC17+4, SS-ROX at 100 K -

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Basic information

Entry
Database: PDB / ID: 6lpl
TitleA2AR crystallized in EROCOC17+4, SS-ROX at 100 K
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / LCP crystallization / Isoprenoid-Chained-Lipid / GPCR / SS-ROX
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 / glutamatergic synapse / lipid binding / 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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)56,05728
Polymers49,9741
Non-polymers6,08327
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint20 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.890, 179.276, 140.956
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
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, 165 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-NA / SODIUM ION


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


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


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


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


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


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


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


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


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 / Tridecane


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM sodium citrate pH5.5, 35-40% PEG400, 50 mM NaSCN, and 2% 2,5-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→42.8 Å / Num. obs: 34815 / % possible obs: 100 % / Redundancy: 49.7 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.991 / R split: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2→2.08 Å / Redundancy: 51.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3765 / CC1/2: 0.472 / R split: 0.638 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

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Processing

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

4eiy


Resolution: 2→42.75 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.749 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1756 5 %RANDOM
Rwork0.173 ---
obs0.1748 33027 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.13 Å2 / Biso mean: 47.033 Å2 / Biso min: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2---1.11 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 431 138 3605
Biso mean--64.97 50.45 -
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_deg1.6841.6564697
X-RAY DIFFRACTIONr_angle_other_deg1.311.6178806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16821.644146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51115517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7541517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 119 -
Rwork0.264 2363 -
all-2482 -
obs--99.92 %

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