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- PDB-8gng: Crystal structure of human adenosine A2A receptor in complex with... -

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Basic information

Entry
Database: PDB / ID: 8gng
TitleCrystal structure of human adenosine A2A receptor in complex with istradefylline.
Components
  • (antibody fab fragment ...) x 2
  • Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / adenosine A2A receptor / istradefylline / neutral antagonist / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
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 / NGF-independant TRKA activation ...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 / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / : / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / synaptic transmission, glutamatergic / central nervous system development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / positive regulation of apoptotic signaling pathway / 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 / calmodulin binding / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / 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-JQ9 / : / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSuzuki, M. / Saito, J. / Miyagi, H. / Yasunaga, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol.Pharmacol. / Year: 2023
Title: In Vitro Pharmacological Profile of KW-6356, a Novel Adenosine A 2A Receptor Antagonist/Inverse Agonist.
Authors: Ohno, Y. / Suzuki, M. / Asada, H. / Kanda, T. / Saki, M. / Miyagi, H. / Yasunaga, M. / Suno, C. / Iwata, S. / Saito, J.I. / Uchida, S.
History
DepositionAug 23, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosine receptor A2a
L: antibody fab fragment light chain
H: antibody fab fragment heavy chain
X: Adenosine receptor A2a
Y: antibody fab fragment light chain
Z: antibody fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,79722
Polymers170,3146
Non-polymers4,48316
Water543
1
A: Adenosine receptor A2a
L: antibody fab fragment light chain
H: antibody fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,75512
Polymers85,1573
Non-polymers2,5989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: Adenosine receptor A2a
Y: antibody fab fragment light chain
Z: antibody fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,04210
Polymers85,1573
Non-polymers1,8857
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.590, 134.840, 42.150
Angle α, β, γ (deg.)97.720, 91.440, 89.380
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21X
12L
22Y
13H
23Z

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA5 - 30812 - 315
21GLYGLYLEULEUXD5 - 30812 - 315
12ASPASPASNASNLB1 - 2121 - 212
22ASPASPASNASNYE1 - 2121 - 212
13GLUGLUARGARGHC1 - 2241 - 224
23GLUGLUARGARGZF1 - 2241 - 224

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AX

#1: Protein Adenosine receptor A2a


Mass: 37333.953 Da / Num. of mol.: 2 / Mutation: A54L, T88A, K122A, N154Q, V239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2 / Production host: Komagataella pastoris (fungus) / References: UniProt: P29274

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Antibody , 2 types, 4 molecules LYHZ

#2: Antibody antibody fab fragment light chain


Mass: 23527.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody antibody fab fragment heavy chain


Mass: 24294.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 5 types, 19 molecules

#4: Chemical ChemComp-JQ9 / 8-[(~{E})-2-(3,4-dimethoxyphenyl)ethenyl]-1,3-diethyl-7-methyl-purine-2,6-dione / istradefylline


Mass: 384.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7 / Details: PEGMME 500, potassium citrate tribasic, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→49.57 Å / Num. obs: 26841 / % possible obs: 99.9 % / Redundancy: 9.2 % / CC1/2: 0.924 / Rmerge(I) obs: 0.662 / Rpim(I) all: 0.225 / Rrim(I) all: 0.701 / Net I/σ(I): 3.9 / Num. measured all: 247473 / Scaling rejects: 408
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.429.12.2924423948530.4440.7862.4291.4100
9.05-49.5710.20.1791205711810.9880.0560.1881099.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VGA

3vga


Resolution: 3.2→49.57 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.825 / SU B: 78.509 / SU ML: 0.567 / SU R Cruickshank DPI: 0.4915 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.603 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2769 1434 5.3 %RANDOM
Rwork0.2181 ---
obs0.2211 25406 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.94 Å2 / Biso mean: 42.243 Å2 / Biso min: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0.44 Å2-0.12 Å2
2---4.46 Å2-0.41 Å2
3---2.38 Å2
Refinement stepCycle: final / Resolution: 3.2→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11097 0 222 3 11322
Biso mean--52.79 16.89 -
Num. residues----1440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311592
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710639
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.65315757
X-RAY DIFFRACTIONr_angle_other_deg1.1951.59724659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60451428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73622.154492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.824151791
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7921549
X-RAY DIFFRACTIONr_chiral_restr0.0580.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022469
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A89020.1
12X89020.1
21L61250.11
22Y61250.11
31H63370.11
32Z63370.11
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 142 -
Rwork0.332 1850 -
all-1992 -
obs--99.95 %
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)
11.1308-0.5950.05091.45340.34681.093-0.0012-0.05880.2650.12610.1193-0.4863-0.06440.0259-0.11810.0527-0.0220.01080.4980.01330.596113.405771.40666.1232
21.2554-0.02730.6491.38450.35311.1518-0.059-0.056-0.0051-0.11160.1658-0.07-0.0177-0.0933-0.10680.0158-0.01520.02150.49150.07780.335710.700131.8926-7.0267
31.2295-0.73750.3831.2902-0.04021.697-0.05850.1254-0.3442-0.1474-0.00290.00740.20090.01060.06140.19770.02610.06710.53650.0590.576217.0097-2.8474-16.1295
41.1774-0.6474-0.13072.1230.2631.0761-0.09140.0516-0.18-0.00280.12550.39450.1369-0.0459-0.03410.0837-0.01280.00830.49370.08840.5764-20.933480.53747.0655
51.15570.4859-0.62133.3988-0.46240.3618-0.18540.004-0.0983-0.38610.2021-0.06830.1277-0.0067-0.01670.1756-0.0327-0.0320.52750.07050.3603-18.0815121.46062.8504
62.08260.255-0.96220.4937-0.3082.42230.00220.11930.2725-0.01610.00650.1914-0.2105-0.1974-0.00870.11180.04050.01820.47830.09930.4587-21.5738157.75813.0014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 401
2X-RAY DIFFRACTION2L1 - 108
3X-RAY DIFFRACTION2H1 - 123
4X-RAY DIFFRACTION3H124 - 224
5X-RAY DIFFRACTION3L109 - 212
6X-RAY DIFFRACTION4X5 - 401
7X-RAY DIFFRACTION5Y1 - 108
8X-RAY DIFFRACTION5Z1 - 123
9X-RAY DIFFRACTION6Z124 - 224
10X-RAY DIFFRACTION6Y109 - 212

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