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- PDB-4eiy: Crystal structure of the chimeric protein of A2aAR-BRIL in comple... -

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Basic information

Entry
Database: PDB / ID: 4eiy
TitleCrystal structure of the chimeric protein of A2aAR-BRIL in complex with ZM241385 at 1.8A resolution
ComponentsAdenosine receptor A2a/Soluble cytochrome b562 chimera
KeywordsMEMBRANE PROTEIN / Novel protein engineering / GPCR Network / PSI-Biology / Structural Genomics / GPCR
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 / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / synaptic transmission, cholinergic / response to caffeine / intermediate filament / 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 / electron transport chain / regulation of mitochondrial membrane potential / locomotory behavior / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / astrocyte activation / positive regulation of synaptic transmission, GABAergic / apoptotic signaling pathway / 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 / neuronal cell body / glutamatergic synapse / apoptotic process / dendrite / lipid binding / 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 c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Adenosine A2A receptor / Adenosine receptor / Cytochrome c/b562 / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CHOLESTEROL / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, W. / Chun, E. / Thompson, A.A. / Chubukov, P. / Xu, F. / Katritch, V. / Han, G.W. / Heitman, L.H. / Ijzerman, A.P. / Cherezov, V. ...Liu, W. / Chun, E. / Thompson, A.A. / Chubukov, P. / Xu, F. / Katritch, V. / Han, G.W. / Heitman, L.H. / Ijzerman, A.P. / Cherezov, V. / Stevens, R.C. / GPCR Network (GPCR)
CitationJournal: Science / Year: 2012
Title: Structural basis for allosteric regulation of GPCRs by sodium ions.
Authors: Liu, W. / Chun, E. / Thompson, A.A. / Chubukov, P. / Xu, F. / Katritch, V. / Han, G.W. / Roth, C.B. / Heitman, L.H. / IJzerman, A.P. / Cherezov, V. / Stevens, R.C.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_radiation_wavelength / entity_src_gen / software
Item: _diffrn_radiation_wavelength.wavelength
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,72231
Polymers49,9741
Non-polymers8,74830
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.442, 179.516, 140.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis:-x,y,-z+1/2

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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 / Mutation: M215W, H310I, R314L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: AA2AR_HUMAN, ADORA2, ADORA2A, cybC / Plasmid: pFASTBAC / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7

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Non-polymers , 8 types, 207 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-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 16 / 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.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#7: 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
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 55

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / pH: 5
Details: 25-28% (v/v) PEG 400, 0.04-0.06M sodium thiocyanate, 2% (v/v) 2,5-hexanediol, 100mM sodium citrate, pH 5.0, Lipid Cubic Phase (LCP), temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.033
SYNCHROTRONAPS 23-ID-D21.033
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDNov 12, 2011
MARMOSAIC 300 mm CCD2CCDDec 10, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21
ReflectionResolution: 1.8→29.73 Å / Num. obs: 44413 / % possible obs: 95.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.8 / % possible all: 92.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EML

3eml


Resolution: 1.8→29.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.764 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. A SODIUM ION IS MODELLED BASED ON CRYSTALLIZATION CONDITION AND COORDINATION GEOMETRY. SODIUM ION IS COORDINATED IN AN OCTAHEDRAL GEOMETRY TO OD1 OF ASP52, OG OF SER 91 AND THREE WATER ...Details: 1. A SODIUM ION IS MODELLED BASED ON CRYSTALLIZATION CONDITION AND COORDINATION GEOMETRY. SODIUM ION IS COORDINATED IN AN OCTAHEDRAL GEOMETRY TO OD1 OF ASP52, OG OF SER 91 AND THREE WATER MOLECULES OF HOH2529, HOH2552 AND HOH2579. 2. THERE IS SOME UNKNOWN AND UNMODELLED DENSITY LOCATED NEAR THE PHENOL RING OF THE ZMA LIGAND, WHICH LIKELY REPRESENT AN ALTERNATIVE CONFORMATION OF THIS FLEXIBLE MOIETY. 3. DISORDERED LIPIDS INCLUDING OLA-2417, OLA-2419, OLC-2423, OLC-2427, OLC-2428 COULD REPRESENT FRAGMENTS OF PHOSPHOLIPID, CHOLESTEROL OR 1-OLEOYL-RAC-GLYCEROL.
RfactorNum. reflection% reflectionSelection details
Rfree0.21313 2222 5 %RANDOM
Rwork0.17407 ---
obs0.17604 42032 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 481 177 3670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223653
X-RAY DIFFRACTIONr_bond_other_d0.0010.022680
X-RAY DIFFRACTIONr_angle_refined_deg1.5842.0654891
X-RAY DIFFRACTIONr_angle_other_deg1.09836560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7115412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74623.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0811516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
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_it1.48132011
X-RAY DIFFRACTIONr_mcbond_other0.453812
X-RAY DIFFRACTIONr_mcangle_it2.2753253
X-RAY DIFFRACTIONr_scbond_it4.02681642
X-RAY DIFFRACTIONr_scangle_it5.791111638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 147 -
Rwork0.273 2809 -
obs--87.95 %
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)
11.30471.6923-0.526420.5751-6.25183.2950.04840.03770.00630.06440.11340.4664-0.133-0.1228-0.16170.05670.0019-0.0020.1036-0.0040.0127-10.9918-3.94546.8744
219.526816.1895-12.942123.952-2.749215.0509-0.95590.0523-0.4134-0.19510.6010.40291.16110.37510.35490.2441-0.0184-0.07660.09490.08450.5072-10.3295-29.831614.7622
31.7642-1.01930.52523.6582-0.8231.3426-0.0068-0.0812-0.0569-0.07160.12310.17180.0548-0.1406-0.11630.0468-0.00170.00430.08530.00830.0164-10.1582-5.018617.3034
43.8666-6.6088-0.21614.96150.19190.8786-0.1526-0.16270.12880.37710.1149-0.36730.08010.0110.03770.0518-0.0024-0.01690.09230.00140.015-1.9496-10.781424.2306
514.8029-10.1338-9.577121.7072-1.242210.3164-0.6072-0.7783-0.491-0.05760.1444-0.02960.62010.66940.46280.3188-0.0056-0.02310.25680.09790.19250.9067-33.068428.5603
61.2035-1.2283-0.100921.4041-1.92290.5095-0.1843-0.0734-0.21070.66210.22880.22350.17490.0245-0.04440.19810.0268-0.00070.11350.02620.0599-7.8641-13.86529.7137
76.1179-3.8313.24953.2583-1.10233.7961-0.38170.18720.90810.1153-0.182-0.1317-0.8552-0.07530.56380.29850.04090.06970.15630.03150.5053-6.981817.066927.1623
84.6764-3.73451.11635.4095-0.44742.36060.03430.00990.0618-0.0091-0.09330.1967-0.12070.01750.0590.0515-0.01360.00540.0812-0.00550.04530.41027.280325.433
92.0881-5.4485-1.602821.86996.20252.4787-0.0124-0.07470.00980.29710.141-0.88250.14980.1408-0.12860.11070.0272-0.02050.1176-0.00980.163913.0473-20.87221.8023
100.720.53370.21626.3930.65480.8604-0.03050.0484-0.1623-0.26630.1347-0.32550.14980.121-0.10420.07310.02990.01150.09460.00510.07427.6709-13.346515.0381
117.0264-4.200310.92828.2942-1.678121.0838-0.9217-0.0670.4910.45950.5554-0.6952-1.28020.41630.36620.27050.03840.03810.19620.0520.205711.139616.208317.3125
120.91282.09470.424213.7331.07451.1449-0.01660.07850.0003-0.4142-0.0077-0.03090.02720.03630.02420.05690.02210.00040.1070.01650.0179-0.4175-5.01658.2951
1322.3732-1.2776.31911.2448-0.048813.30270.21631.142-0.7201-0.983-0.0720.53610.6687-0.3328-0.14430.3223-0.0784-0.02270.1721-0.04360.1214-10.487-25.22072.7877
1414.3514-19.9233-1.910138.52121.48381.76640.27250.1460.435-0.989-0.5419-1.66470.18720.1640.26940.28870.06650.10440.24150.01850.637125.7603-49.398516.1997
1517.2785-13.6158-2.749224.2101-4.79616.769-0.4648-1.17991.76581.07320.6136-1.4639-0.50010.2215-0.14880.35480.0591-0.21180.3251-0.22130.861524.5547-53.445425.5883
1627.1612-17.41078.321623.1118-9.620413.8851-0.4466-1.3740.1430.65831.31321.4145-0.2563-1.0919-0.86650.23750.05510.04970.28310.07720.524415.0374-57.940323.7417
1724.1901-14.50386.775918.4892-2.994814.5502-0.3005-0.46490.2023-0.7867-0.0522-0.10430.72660.21250.35270.28930.07630.02260.1325-0.01420.455726.536-65.965918.9084
1811.3951-14.29368.210432.80261.701715.61221.43330.4974-0.6457-1.9857-0.47320.21070.8320.4045-0.96010.45620.059-0.12230.1950.07220.6115.9315-55.60112.964
1944.08987.508-6.95240.5722-11.064116.1501-0.2723-0.4155-1.6832-1.7480.16610.46820.53120.05610.10620.35480.0913-0.150.12070.00820.544711.8641-47.55513.4572
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 DIFFRACTION16A1058 - 1081
17X-RAY DIFFRACTION17A1082 - 1093
18X-RAY DIFFRACTION18A1094 - 1101
19X-RAY DIFFRACTION19A1102 - 1106

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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