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- PDB-5jtb: Crystal structure of the chimeric protein of A2aAR-BRIL with boun... -

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Basic information

Entry
Database: PDB / ID: 5jtb
TitleCrystal structure of the chimeric protein of A2aAR-BRIL with bound iodide ions
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / iodide
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 / response to caffeine / blood circulation / 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 synaptic transmission, GABAergic / positive regulation of protein secretion / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / excitatory postsynaptic potential / apoptotic signaling pathway / locomotory behavior / electron transport chain / negative regulation of inflammatory response / vasodilation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / electron transfer activity / periplasmic space / 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 / heme binding / apoptotic process / dendrite / regulation of DNA-templated transcription / lipid binding / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
CHOLESTEROL / IODIDE ION / OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / DI(HYDROXYETHYL)ETHER / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMelnikov, I. / Polovinkin, V. / Shevtsov, M. / Borshchevskiy, V. / Cherezov, V. / Popov, A. / Gordeliy, V.
CitationJournal: Sci Adv / Year: 2017
Title: Fast iodide-SAD phasing for high-throughput membrane protein structure determination.
Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G. ...Authors: Melnikov, I. / Polovinkin, V. / Kovalev, K. / Gushchin, I. / Shevtsov, M. / Shevchenko, V. / Mishin, A. / Alekseev, A. / Rodriguez-Valera, F. / Borshchevskiy, V. / Cherezov, V. / Leonard, G.A. / Gordeliy, V. / Popov, A.
History
DepositionMay 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)56,07124
Polymers49,9741
Non-polymers6,09723
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint48 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.648, 179.793, 139.810
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 / Cytochrome b-562


Mass: 49974.281 Da / Num. of mol.: 1
Fragment: UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316,UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316,UNP Residues 2-208,UNP Residues 23-217,UNP Residues 219-316
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, 87 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-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O2
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#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.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.85 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.85 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 23712 / % possible obs: 0.997 % / Redundancy: 6.87 % / CC1/2: 0.997 / Rmerge(I) obs: 0.185 / Net I/σ(I): 8.83
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→89.9 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.869 / SU B: 28.975 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29444 661 5.2 %RANDOM
Rwork0.23445 ---
obs0.2377 12126 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0 Å2
2---0.08 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.8→89.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 329 64 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3392.0154636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9495392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02623.411129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34915515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1731518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212418
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4382.2221556
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8263.3241943
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2962.7041883
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.41418.6895098
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 48 -
Rwork0.243 856 -
obs--97.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3461-1.33660.2576.3413-1.61720.8514-0.0526-0.08420.0174-0.13290.19660.03320.0733-0.1493-0.1440.1360.0299-0.00390.2073-0.0020.1058-11.06624.512762.9214
24.3411-5.40422.19559.2817-5.16593.42890.23060.4830.22720.0712-0.2351-0.1457-0.2153-0.08840.00450.16870.06870.05370.28540.11090.2833-10.291329.789955.0501
30.4767-0.2947-0.24710.3612-0.09630.5405-0.0270.0078-0.00410.12540.02640.0177-0.0527-0.08390.00060.1767-0.003-0.01350.1919-0.00940.1335-10.16024.995952.7144
41.4882.5220.07065.04810.10420.1718-0.08620.112-0.0721-0.09740.0477-0.2570.03230.00640.03850.1154-0.02720.00710.21860.01780.1009-1.984710.601745.7304
54.11650.94052.4926.5954-1.54172.2089-0.03480.25880.10240.2281-0.0614-0.0553-0.10630.18040.09610.1946-0.03270.00760.24320.02210.11460.118532.625441.4846
60.0133-0.08740.05666.517-4.12022.6097-0.0482-0.0010.0292-0.33540.23750.2630.1914-0.1592-0.18930.21310.0004-0.07290.18640.01210.1493-7.781512.964740.1847
75.82697.74692.28510.4093.27171.4038-0.29060.39980.3626-0.0770.47790.35780.45360.0808-0.18740.70540.0152-0.24530.21120.19680.304-7.7851-17.232342.7235
82.88011.14760.59271.6923-0.43240.49130.2043-0.07330.0544-0.0041-0.22910.05860.09780.0880.02480.1189-0.0040.04870.2364-0.02510.07950.3068-7.331944.6593
91.15391.95980.4236.18083.28652.4926-0.07540.2556-0.1176-0.00060.4002-0.52250.02770.1043-0.32470.1684-0.0382-0.03120.1698-0.0150.170212.79920.708448.2476
100.8191-0.58370.18030.8837-0.64730.6251-0.2447-0.26180.07450.31170.1699-0.1273-0.1882-0.02560.07480.20080.0113-0.07320.2541-0.05940.08797.471812.97954.782
112.39281.5672-3.00053.25352.784713.9279-0.1243-0.2359-0.1623-0.1171-0.1074-0.06520.11550.36320.23170.17250.0099-0.01910.16820.04230.140610.9941-16.29553.0568
120.2359-1.0239-0.20196.08650.11750.5288-0.016-0.0129-0.04320.1553-0.02690.131-0.01870.02940.0430.122300.00040.20460.00720.1346-0.59185.05461.5607
136.51340.17981.6363.0271-1.41534.2008-0.0297-0.38380.25160.24830.11570.1327-0.3621-0.1491-0.0860.14590.05260.00220.171-0.01210.0887-10.538625.280666.9777
145.08956.4834-0.81258.8186-0.5220.68590.14030.01540.04780.2915-0.00890.01180.02580.0507-0.13140.0907-0.0290.00110.1493-0.01520.260925.555549.007553.0354
155.93285.07521.29446.7089-2.20925.8253-0.27240.014-0.4646-0.59-0.0991-0.39270.51160.33920.37150.086-0.01150.10510.1717-0.0440.430624.440253.802744.4831
164.44353.3995-2.36485.6407-3.17632.3406-0.21070.17550.352-0.5760.44260.43810.31540.096-0.23190.0779-0.04580.00630.27280.02290.226516.925859.227446.2304
174.20562.21171.15016.18141.9430.6729-0.1260.2782-0.42120.4040.2503-0.33450.0930.1007-0.12430.0646-0.04820.01310.20260.01720.248826.574865.557451.3657
181.58310.31254.00563.1464-3.030714.98060.0868-0.08250.0959-0.0865-0.2267-0.01670.46470.09640.13980.17660.0408-0.0350.1427-0.03920.333215.590355.466856.9036
198.46882.05073.100718.83292.31592.3172-0.03680.4208-0.27050.29530.1434-0.6915-0.01460.0891-0.10660.1678-0.02560.00490.1554-0.0170.160712.448746.921755.8512
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 34
2X-RAY DIFFRACTION2A35 - 38
3X-RAY DIFFRACTION3A39 - 73
4X-RAY DIFFRACTION4A74 - 108
5X-RAY DIFFRACTION5A109 - 117
6X-RAY DIFFRACTION6A118 - 137
7X-RAY DIFFRACTION7A138 - 161
8X-RAY DIFFRACTION8A162 - 186
9X-RAY DIFFRACTION9A187 - 208
10X-RAY DIFFRACTION10A219 - 259
11X-RAY DIFFRACTION11A260 - 265
12X-RAY DIFFRACTION12A266 - 292
13X-RAY DIFFRACTION13A293 - 307
14X-RAY DIFFRACTION14A1001 - 1021
15X-RAY DIFFRACTION15A1022 - 1042
16X-RAY DIFFRACTION16A1060 - 1081
17X-RAY DIFFRACTION17A1082 - 1093
18X-RAY DIFFRACTION18A1094 - 1101
19X-RAY DIFFRACTION19A1102 - 1106

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