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- PDB-8wdt: Crystal structure of the human adenosine A2A receptor in complex ... -

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Basic information

Entry
Database: PDB / ID: 8wdt
TitleCrystal structure of the human adenosine A2A receptor in complex with photoresponsive ligand photoNECA(blue)
Components
  • Adenosine receptor A2a
  • Antibody Fab fragment heavy chain
  • Antibody Fab fragment light chain
KeywordsMEMBRANE PROTEIN / G-protein coupled receptor / GPCR
Function / homology
Function and homology information


regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / positive regulation of acetylcholine secretion, neurotransmission / 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 / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / positive regulation of acetylcholine secretion, neurotransmission / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / intermediate filament / presynaptic active zone / positive regulation of urine volume / response to caffeine / blood circulation / sensory perception / positive regulation of glutamate secretion / eating behavior / inhibitory postsynaptic potential / regulation of calcium ion transport / alpha-actinin binding / asymmetric synapse / axolemma / membrane depolarization / cellular defense response / prepulse inhibition / phagocytosis / neuron projection morphogenesis / positive regulation of synaptic transmission, glutamatergic / astrocyte activation / presynaptic modulation of chemical synaptic transmission / positive regulation of long-term synaptic potentiation / positive regulation of synaptic transmission, GABAergic / central nervous system development / positive regulation of protein secretion / response to amphetamine / regulation of mitochondrial membrane potential / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / synaptic transmission, glutamatergic / excitatory postsynaptic potential / locomotory behavior / negative regulation of inflammatory response / vasodilation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / blood coagulation / cell-cell signaling / adenylate cyclase-activating G protein-coupled receptor signaling pathway / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / calmodulin binding / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / regulation of DNA-templated transcription / lipid binding / dendrite / protein-containing complex binding / glutamatergic synapse / enzyme binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / 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
Chem-WCH / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsAraya, T. / Asada, H. / Iwata, S. / Im, D.H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A 2A receptor.
Authors: Araya, T. / Matsuba, Y. / Suzuki, H. / Doura, T. / Nuemket, N. / Nango, E. / Yamamoto, M. / Im, D. / Asada, H. / Kiyonaka, S. / Iwata, S.
History
DepositionSep 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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
B: Antibody Fab fragment light chain
C: Antibody Fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1974
Polymers86,7853
Non-polymers4121
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)372.640, 52.520, 63.400
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adenosine receptor A2a


Mass: 39114.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274
#2: Antibody Antibody Fab fragment light chain


Mass: 23356.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Antibody Fab fragment heavy chain


Mass: 24314.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-WCH / (2S,3S,4R,5R)-5-(6-amino-2-((E)-phenyldiazenyl)-9H-purin-9-yl)-N-ethyl-3,4-dihydroxytetrahydrofuran-2-carboxamide


Mass: 412.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N8O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 3.56 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: 0.1 M Sodium citrate, 0.005-0.03 M Magnesium chloride hexahydrate, 0.15 M Sodium chloride, 27.5-29.0% PEG500DME

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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: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.34→46.42 Å / Num. obs: 18172 / % possible obs: 99.71 % / Redundancy: 65.4 % / Biso Wilson estimate: 61.79 Å2 / CC1/2: 0.944 / CC star: 0.985 / Rpim(I) all: 0.1322 / Net I/σ(I): 9.16
Reflection shellResolution: 3.34→3.46 Å / Redundancy: 62.3 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1765 / CC1/2: 0.458 / CC star: 0.793 / Rpim(I) all: 1.5 / % possible all: 99.21

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2-3874phasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→46.42 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1836 10.12 %Random selection
Rwork0.2141 ---
obs0.2194 18137 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.34→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5626 0 30 0 5656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025813
X-RAY DIFFRACTIONf_angle_d0.4777931
X-RAY DIFFRACTIONf_dihedral_angle_d10.0752018
X-RAY DIFFRACTIONf_chiral_restr0.039918
X-RAY DIFFRACTIONf_plane_restr0.003985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.34-3.430.33951430.28761207X-RAY DIFFRACTION99
3.43-3.530.3191350.28541245X-RAY DIFFRACTION100
3.53-3.640.31061430.25281202X-RAY DIFFRACTION100
3.65-3.780.31471330.25931278X-RAY DIFFRACTION100
3.78-3.930.30081390.25351244X-RAY DIFFRACTION100
3.93-4.10.31671420.21291237X-RAY DIFFRACTION100
4.1-4.320.24191370.18691256X-RAY DIFFRACTION100
4.32-4.590.21841410.17851256X-RAY DIFFRACTION100
4.59-4.950.19361460.1731243X-RAY DIFFRACTION100
4.95-5.440.21731400.16691259X-RAY DIFFRACTION100
5.44-6.230.24821360.21191270X-RAY DIFFRACTION100
6.23-7.840.25141470.22411278X-RAY DIFFRACTION100
7.84-46.420.28981540.20421326X-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)
12.68370.4203-2.334.85681.16022.43390.26360.0707-2.17550.4949-0.4060.55840.59210.9362-0.1350.64520.44080.17041.19520.4081.3559-34.758214.342240.9294
24.44190.9632-0.29973.21310.64972.2043-0.08180.4797-0.3577-0.0455-0.0756-0.4489-0.09850.84560.1280.32880.0450.05810.97460.18530.6643-37.503330.089634.7778
34.6777-1.7838-3.44311.93551.06252.6176-0.63840.9033-0.12690.2094-0.3048-1.3794-0.4351.23640.60770.8253-0.03760.10621.82040.0491.2202-10.043132.028836.4376
44.5286-0.4438-0.8191.090.35682.2867-0.0862-0.80940.29580.4010.1868-0.3384-0.0850.97310.06480.36650.01390.00470.96530.12631.0945-40.852838.000948.1291
58.0061-3.60930.42992.4273-0.37541.47060.4057-0.63420.0742-0.1674-0.2234-0.46250.16251.2071-0.0910.5640.06990.16221.21550.20760.6068-42.919632.93549.4218
68.1892-0.48660.20735.41291.0592.51480.3411-1.53711.05250.7605-0.6679-0.5703-0.00270.7310.21290.66520.1073-0.03851.57460.54410.822-31.019124.717749.9987
77.65840.82896.06066.3554-0.33745.9963-0.031.0667-4.17581.4132-0.75920.49781.95081.3250.88520.89750.20960.55361.51070.25862.4798-54.190111.663539.2319
81.6873-0.1231-1.09645.5559-5.91258.48970.4409-0.49650.27010.6356-0.1611-0.0129-0.9340.491-0.24070.4327-0.02450.13670.43320.07580.5345-90.547261.134556.7768
93.56632.1244-0.03736.67771.91013.44740.1082-0.5751-1.0819-0.58740.5734-1.4018-0.03030.32190.64930.3107-0.06660.16810.21570.1550.4015-82.867554.916456.0536
105.39421.38242.71922.55720.62263.13050.29411.10570.3791-1.1063-0.4108-0.6863-0.31880.86460.00380.41370.02320.21370.13190.00290.6279-84.634455.15844.3893
115.3929-3.4133-0.01965.232-1.18330.78220.0167-0.46751.25940.61850.4597-0.7414-0.8799-0.22390.9979-0.0251-0.07240.32010.27650.10220.9138-80.362560.752654.6687
125.13450.86732.13986.49880.85495.40860.4731.16890.2243-1.0261-0.53630.7123-0.4120.91450.10520.33720.07240.02480.35360.02980.4492-89.524559.807347.9923
134.0826-4.46462.8216.4838-3.24252.0302-0.1336-0.0496-0.11110.0314-0.0596-0.3686-0.3062-0.00840.10330.35630.06120.22120.41360.05210.4615-93.689357.31553.4712
144.13315.0462-0.97327.6894-3.70874.8283-0.01270.6725-1.2989-1.24520.5188-0.64170.5793-0.7154-0.10240.4356-0.21750.1120.53540.03640.6355-130.573354.103345.1013
158.24453.20782.72576.52172.65083.48190.40570.5256-0.00020.47750.06630.57360.4036-0.3461-0.39150.28530.02630.02070.29320.17640.3417-117.26462.791849.8363
163.59911.6021.88176.4891-1.2431.75820.1514-1.67770.5691.1429-0.14320.8599-1.0752-1.9372-0.20520.4273-0.01140.12350.99110.10150.3597-128.601263.616758.8993
173.72783.9633-4.86394.4913-5.85337.99460.18780.54710.0187-0.45410.22970.5958-0.0619-0.902-0.14280.5292-0.00810.05410.4059-0.03070.4545-112.168259.907349.3642
188.48012.17160.96863.57030.11936.45870.7525-1.654-1.46290.339-0.22980.83580.6998-0.9771-0.27330.4384-0.20170.09790.49080.10830.8602-130.407153.404953.4979
198.48255.46781.4846.00243.88146.59010.4947-1.0327-0.11110.5596-0.22110.5328-0.401-1.5533-0.16860.3515-0.04240.08490.65250.22530.958-132.846662.251154.8793
205.35434.54341.87087.85691.19574.7684-0.19231.38610.99550.77490.08491.844-0.0179-1.04720.2910.42620.0127-0.0090.6402-0.08440.5656-128.153568.58650.3973
214.40964.46641.82457.6359-0.55112.86230.1398-0.0057-0.6018-0.0953-0.2955-0.19510.23120.2990.20450.41140.0450.03340.22890.02380.3265-88.323236.608347.6027
224.0472-3.4045-2.40834.08734.55868.14080.1663-0.1233-0.02150.03740.2164-0.29350.7741-0.2433-0.33980.5956-0.01680.04870.27670.07580.6164-85.230329.927953.1258
236.2064-3.64090.99452.2915-0.05250.4260.18540.17330.2514-0.208-0.0955-0.04040.0203-0.105-0.02790.5116-0.01940.07060.29340.00370.231-100.38742.961745.9258
244.8805-2.01011.71166.1674-0.57680.58120.3298-0.1285-1.4577-1.64960.07930.33010.90050.2698-0.4070.81480.13490.03580.37170.05880.9033-117.536446.389441.4922
257.6007-0.86210.46458.69720.86543.14760.72670.0364-1.45050.5886-0.173-0.305-0.2731-0.2935-0.35440.4818-0.0003-0.10430.33420.07050.5962-116.017950.454845.3456
263.2074-1.44741.1661.0614-1.5543.5430.02620.8219-1.1087-0.46330.1781-0.61920.69220.3318-0.10780.60290.1502-0.06410.4998-0.10740.8133-123.284152.261633.6959
272.4715-1.203-1.45210.58580.70680.8511-0.1753-0.5504-0.77720.51990.2607-0.0976-0.04350.4179-0.00560.47980.5363-0.28560.74360.0680.8954-141.526555.712540.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 165 )
4X-RAY DIFFRACTION4chain 'A' and (resid 166 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 258 )
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 292 )
7X-RAY DIFFRACTION7chain 'A' and (resid 293 through 307 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 18 )
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 37 )
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 60 )
11X-RAY DIFFRACTION11chain 'B' and (resid 61 through 74 )
12X-RAY DIFFRACTION12chain 'B' and (resid 75 through 89 )
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 112 )
14X-RAY DIFFRACTION14chain 'B' and (resid 113 through 127 )
15X-RAY DIFFRACTION15chain 'B' and (resid 128 through 143 )
16X-RAY DIFFRACTION16chain 'B' and (resid 144 through 154 )
17X-RAY DIFFRACTION17chain 'B' and (resid 155 through 173 )
18X-RAY DIFFRACTION18chain 'B' and (resid 174 through 185 )
19X-RAY DIFFRACTION19chain 'B' and (resid 186 through 196 )
20X-RAY DIFFRACTION20chain 'B' and (resid 197 through 213 )
21X-RAY DIFFRACTION21chain 'C' and (resid 15 through 53 )
22X-RAY DIFFRACTION22chain 'C' and (resid 54 through 74 )
23X-RAY DIFFRACTION23chain 'C' and (resid 75 through 146 )
24X-RAY DIFFRACTION24chain 'C' and (resid 147 through 164 )
25X-RAY DIFFRACTION25chain 'C' and (resid 165 through 187 )
26X-RAY DIFFRACTION26chain 'C' and (resid 188 through 221 )
27X-RAY DIFFRACTION27chain 'C' and (resid 222 through 224 )

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