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- PDB-6jzh: Structure of human A2A adenosine receptor in complex with ZM24138... -

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Basic information

Entry
Database: PDB / ID: 6jzh
TitleStructure of human A2A adenosine receptor in complex with ZM241385 obtained from SFX experiments under atmospheric pressure
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / X-ray free-electron lasers room-temperature G-protein-coupled receptor
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / 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 / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / 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 / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / 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 / lipid binding / glutamatergic synapse / 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
CHOLESTEROL / OLEIC ACID / 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: 2.25 Å
AuthorsNango, E. / Shimamura, T. / Nakane, T. / Yamanaka, Y. / Mori, C. / Kimura, K.T. / Fujiwara, T. / Tanaka, T. / Iwata, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS) Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)X-ray Free-Electron Laser Priority Strategy Program Japan
CitationJournal: J.Appl.Crystallogr. / Year: 2019
Title: High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure.
Authors: Shimazu, Y. / Tono, K. / Tanaka, T. / Yamanaka, Y. / Nakane, T. / Mori, C. / Terakado Kimura, K. / Fujiwara, T. / Sugahara, M. / Tanaka, R. / Doak, R.B. / Shimamura, T. / Iwata, S. / Nango, E. / Yabashi, M.
History
DepositionMay 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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 / _citation_author.name
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)56,87525
Polymers49,9881
Non-polymers6,88724
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint54 kcal/mol
Surface area20320 Å2
Unit cell
Length a, b, c (Å)40.170, 179.590, 142.080
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


Mass: 49988.305 Da / Num. of mol.: 1 / Mutation: N154Q,M29W,H124I,R128L
Source method: isolated from a genetically manipulated source
Details: Chimera of Adenosine receptor A2a and Soluble cytochrome b562
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 5 types, 90 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 / ZM-241,385


Mass: 337.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H15N7O2 / Comment: antagonist*YM
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 27% (v/v) PEG400, 50-mM sodium thiocyanate, 2% (v/v) 2,5-hexanediol, 100-mM sodium citrate (pH 5.0)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.77 Å
DetectorType: MPCCD / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.25→44.9 Å / Num. obs: 25057 / % possible obs: 100 % / Redundancy: 139 % / CC1/2: 0.97 / Net I/σ(I): 5.9
Reflection shellResolution: 2.25→2.29 Å / CC1/2: 0.811
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EIY

4eiy


Resolution: 2.25→33.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.2182 1212 4.85 %
Rwork0.1829 --
obs0.1846 25002 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→33.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 379 66 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033374
X-RAY DIFFRACTIONf_angle_d0.6524539
X-RAY DIFFRACTIONf_dihedral_angle_d10.3372576
X-RAY DIFFRACTIONf_chiral_restr0.044523
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.34010.25891220.21332591X-RAY DIFFRACTION100
2.3401-2.44660.22431740.19452555X-RAY DIFFRACTION100
2.4466-2.57550.22641250.18012614X-RAY DIFFRACTION100
2.5755-2.73680.20991210.18412619X-RAY DIFFRACTION100
2.7368-2.9480.19631290.16712631X-RAY DIFFRACTION100
2.948-3.24450.21131540.17462606X-RAY DIFFRACTION100
3.2445-3.71340.19721330.17312676X-RAY DIFFRACTION100
3.7134-4.67650.22521170.16482694X-RAY DIFFRACTION100
4.6765-33.35980.22721370.20672804X-RAY DIFFRACTION99

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