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- PDB-7ezc: Adenosine A2a receptor mutant-I92N -

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Basic information

Entry
Database: PDB / ID: 7ezc
TitleAdenosine A2a receptor mutant-I92N
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsSIGNALING PROTEIN / GPCR / Adenosine / agonist / active mutation
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
Chem-UKA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsCui, M. / Zhou, Q. / Yao, D. / Zhao, S. / Song, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770898 China
CitationJournal: Iucrj / Year: 2022
Title: Crystal structure of a constitutive active mutant of adenosine A 2A receptor.
Authors: Cui, M. / Zhou, Q. / Xu, Y. / Weng, Y. / Yao, D. / Zhao, S. / Song, G.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562
B: Adenosine receptor A2a,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8744
Polymers96,3182
Non-polymers1,5562
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-9 kcal/mol
Surface area37030 Å2
Unit cell
Length a, b, c (Å)71.230, 175.730, 112.710
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562 / Cytochrome b-562


Mass: 48158.934 Da / Num. of mol.: 2 / Mutation: I92N,M1007W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7
#2: Chemical ChemComp-UKA / 6-(2,2-diphenylethylamino)-9-[(2R,3R,4S,5S)-5-(ethylcarbamoyl)-3,4-dihydroxy-oxolan-2-yl]-N-[2-[(1-pyridin-2-ylpiperidin-4-yl)carbamoylamino]ethyl]purine-2-carboxamide


Mass: 777.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H47N11O6 / Comment: agonist*YM
Has ligand of interestN
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: 3.98 Å3/Da / Density % sol: 69.09 %
Crystal growTemperature: 291 K / Method: lipidic cubic phase / pH: 8.2
Details: 100 mM Tris pH 8.2, 30% PEG400 and 0.4 M (NH4)2SO4.
PH range: 8.0-8.4

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 12, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→47.429 Å / Num. obs: 13682 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 43.4 % / Biso Wilson estimate: 105.9 Å2 / Net I/σ(I): 10.46
Reflection shellResolution: 3.8→3.94 Å / Mean I/σ(I) obs: 1.52

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QAK

3qak


Resolution: 3.8→47.43 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 40.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.313 691 5.07 %
Rwork0.288 --
obs0.289 13628 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.3 Å2
Refinement stepCycle: LAST / Resolution: 3.8→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 114 0 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036024
X-RAY DIFFRACTIONf_angle_d0.6358230
X-RAY DIFFRACTIONf_dihedral_angle_d15.9423486
X-RAY DIFFRACTIONf_chiral_restr0.038981
X-RAY DIFFRACTIONf_plane_restr0.0031020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-4.09340.3891370.35932576X-RAY DIFFRACTION100
4.0934-4.5050.36311380.32072597X-RAY DIFFRACTION100
4.505-5.15620.26211350.29222557X-RAY DIFFRACTION99
5.1562-6.49360.35681400.32542588X-RAY DIFFRACTION100
6.4936-47.4290.28031410.23252619X-RAY DIFFRACTION100
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)
13.1956-0.1204-3.01692.9713-1.76932.99540.14240.3537-0.3107-0.0592-0.22192.0286-0.2388-0.6470.01651.21280.0689-0.54760.88950.09181.29775.493-39.37928.552
26.0425-0.0732-3.73188.0472-2.33212.4092-0.51310.0182-0.4255-1.68370.24590.8818-0.0371-0.1970.13191.2582-0.0707-0.31650.82690.03820.510617.471-46.32126.407
31.75940.6278-1.55622.60920.59951.0751-0.7561-0.15550.38890.33030.9541.4322-0.53270.3416-0.46841.3156-0.0815-0.40960.93780.11751.044121.068-21.09639.539
44.9389-0.1768-0.64164.9882-3.21472.2468-1.2222-0.32562.3131-1.031-0.92771.08821.1896-0.55391.19291.1728-0.00240.14941.4785-0.30111.213114.037-42.64742.997
54.43081.80992.37524.29491.56521.5664-1.0901-0.2653-0.298-0.6278-1.2635-0.31871.8961-0.24810.91742.2188-0.18470.7611.6456-0.09571.13325.409-40.20938.277
60.0270.0546-0.07291.9157-2.73784.6172-0.6178-0.484-0.7592-2.0502-0.60591.76871.1660.9762-0.0920.3771-0.1085-0.13031.6857-0.73591.4487-4.455-20.7831.838
73.4876-3.76550.93014.8585-1.86681.0293-1.26050.0819-1.4206-0.42951.65632.3546-0.55430.5241-0.51031.6372-0.20290.05381.0422-0.2210.854226.5393.10347.304
84.15010.4738-1.59544.22590.04524.7067-0.1916-0.30820.70470.54220.0651.22420.0327-0.27090.28771.158-0.0404-0.12810.77620.08681.299131.53910.45239.592
95.66381.1614-2.16559.3177-2.68024.07140.00720.2728-0.3829-2.2606-0.1094-0.9384-0.23820.13440.22841.4419-0.1970.02930.9185-0.08650.667136.708-47.3115.074
10-0.6185-2.9278-0.28753.3472-1.06621.4744-0.8843-0.15960.4040.53750.233-1.4562-0.42530.3380.16771.184-0.0972-0.26851.1920.25961.49841.595-53.08131.636
113.9147-4.45733.44897.8966-1.29856.7296-0.5184-0.4402-5.70080.0005-0.91882.14742.45850.61110.12931.26280.19820.68491.03070.85572.314146.611-35.89923.019
121.09482.59831.89851.88857.58085.589-4.0466-3.107-1.5106-0.93453.161.0021-2.5098-1.2417-0.28221.33120.67730.9722.05350.2392.265451.853-66.92413.102
130.10830.6909-0.07511.9712-1.7590.1863-0.27360.4554-0.36120.4985-0.8429-0.70130.02360.470.95051.4655-0.1456-0.05061.14120.19661.437644.417-86.76254.177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:107 )A3 - 107
2X-RAY DIFFRACTION2( CHAIN A AND RESID 108:186 )A108 - 186
3X-RAY DIFFRACTION3( CHAIN A AND RESID 187:226 )A187 - 226
4X-RAY DIFFRACTION4( CHAIN A AND RESID 227:268 )A227 - 268
5X-RAY DIFFRACTION5( CHAIN A AND RESID 269:289 )A269 - 289
6X-RAY DIFFRACTION6( CHAIN A AND RESID 290:307 )A290 - 307
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1001:1018 )A0
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1019:1093 )A0
9X-RAY DIFFRACTION9( CHAIN B AND RESID 3:173 )B3 - 173
10X-RAY DIFFRACTION10( CHAIN B AND RESID 174:251 )B174 - 251
11X-RAY DIFFRACTION11( CHAIN B AND RESID 252:287 )B252 - 287
12X-RAY DIFFRACTION12( CHAIN B AND RESID 288:308 )B288 - 308
13X-RAY DIFFRACTION13( CHAIN B AND RESID 1001:1095 )B0

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