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

ID or keywords:

Entry

Database: PDB / ID: 8wdt

Title

Crystal 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

Keywords

MEMBRANE PROTEIN / G-protein coupled receptor / 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 / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / synaptic transmission, cholinergic / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / 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 / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.34 Å

Authors

Araya, T. / Asada, H. / Iwata, S. / Im, D.H.

Funding support

Japan, 2items

Citation

Journal: 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

Deposition	Sep 16, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wdt.cif.gz	301.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8wdt.ent.gz	244.6 KB	Display	PDB format
PDBx/mmJSON format	8wdt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wdt_validation.pdf.gz	679.4 KB	Display	wwPDB validaton report
Full document	8wdt_full_validation.pdf.gz	687.5 KB	Display
Data in XML	8wdt_validation.xml.gz	26.4 KB	Display
Data in CIF	8wdt_validation.cif.gz	35.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wd/8wdt ftp://data.pdbj.org/pub/pdb/validation_reports/wd/8wdt	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #147 - Mar 2012 Rhodopsin similarity (6) #217 - Jan 2018 Opioid Receptors similarity (6) #100 - Apr 2008 Adrenergic Receptors similarity (6) #164 - Aug 2013 Serotonin Receptor similarity (6) #68 - Aug 2005 Neurotrophins similarity (1) #136 - Apr 2011 Nanobodies similarity (6) #27 - Mar 2002 Bacteriorhodopsin similarity (6) #58 - Oct 2004 G Proteins similarity (6) #66 - Jun 2005 Carotenoid Oxygenase similarity (6)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#147 - Mar 2012
Rhodopsin
similarity (6)
#217 - Jan 2018
Opioid Receptors
similarity (6)
#100 - Apr 2008
Adrenergic Receptors
similarity (6)
#164 - Aug 2013
Serotonin Receptor
similarity (6)
#68 - Aug 2005
Neurotrophins
similarity (1)
#136 - Apr 2011
Nanobodies
similarity (6)
#27 - Mar 2002
Bacteriorhodopsin
similarity (6)
#58 - Oct 2004
G Proteins
similarity (6)
#66 - Jun 2005
Carotenoid Oxygenase
similarity (6)

Deposited unit

A: Adenosine receptor A2a

B: Antibody Fab fragment light chain

C: Antibody Fab fragment heavy chain

hetero molecules

87.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	5
Space group name H-M	C121

#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 interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.56 Å³/Da / Density % sol: 60.21 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.34→46.42 Å / Num. obs: 18172 / % possible obs: 99.71 % / Redundancy: 65.4 % / B_iso Wilson estimate: 61.79 Å² / CC_1/2: 0.944 / CC star: 0.985 / R_pim(I) all: 0.1322 / Net I/σ(I): 9.16
Reflection shell	Resolution: 3.34→3.46 Å / Redundancy: 62.3 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 1765 / CC_1/2: 0.458 / CC star: 0.793 / R_pim(I) all: 1.5 / % possible all: 99.21

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18.2-3874	phasing
Coot		model building
PDB_EXTRACT		data extraction

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2659	1836	10.12 %	Random selection
R_work	0.2141	-	-	-
obs	0.2194	18137	99.77 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.34→46.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5626	0	30	0	5656

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5813
X-RAY DIFFRACTION	f_angle_d	0.477	7931
X-RAY DIFFRACTION	f_dihedral_angle_d	10.075	2018
X-RAY DIFFRACTION	f_chiral_restr	0.039	918
X-RAY DIFFRACTION	f_plane_restr	0.003	985

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.34-3.43	0.3395	143	0.2876	1207	X-RAY DIFFRACTION	99
3.43-3.53	0.319	135	0.2854	1245	X-RAY DIFFRACTION	100
3.53-3.64	0.3106	143	0.2528	1202	X-RAY DIFFRACTION	100
3.65-3.78	0.3147	133	0.2593	1278	X-RAY DIFFRACTION	100
3.78-3.93	0.3008	139	0.2535	1244	X-RAY DIFFRACTION	100
3.93-4.1	0.3167	142	0.2129	1237	X-RAY DIFFRACTION	100
4.1-4.32	0.2419	137	0.1869	1256	X-RAY DIFFRACTION	100
4.32-4.59	0.2184	141	0.1785	1256	X-RAY DIFFRACTION	100
4.59-4.95	0.1936	146	0.173	1243	X-RAY DIFFRACTION	100
4.95-5.44	0.2173	140	0.1669	1259	X-RAY DIFFRACTION	100
5.44-6.23	0.2482	136	0.2119	1270	X-RAY DIFFRACTION	100
6.23-7.84	0.2514	147	0.2241	1278	X-RAY DIFFRACTION	100
7.84-46.42	0.2898	154	0.2042	1326	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	2.6837	0.4203	-2.33	4.8568	1.1602	2.4339	0.2636	0.0707	-2.1755	0.4949	-0.406	0.5584	0.5921	0.9362	-0.135	0.6452	0.4408	0.1704	1.1952	0.408	1.3559	-34.7582	14.3422	40.9294
2	4.4419	0.9632	-0.2997	3.2131	0.6497	2.2043	-0.0818	0.4797	-0.3577	-0.0455	-0.0756	-0.4489	-0.0985	0.8456	0.128	0.3288	0.045	0.0581	0.9746	0.1853	0.6643	-37.5033	30.0896	34.7778
3	4.6777	-1.7838	-3.4431	1.9355	1.0625	2.6176	-0.6384	0.9033	-0.1269	0.2094	-0.3048	-1.3794	-0.435	1.2364	0.6077	0.8253	-0.0376	0.1062	1.8204	0.049	1.2202	-10.0431	32.0288	36.4376
4	4.5286	-0.4438	-0.819	1.09	0.3568	2.2867	-0.0862	-0.8094	0.2958	0.401	0.1868	-0.3384	-0.085	0.9731	0.0648	0.3665	0.0139	0.0047	0.9653	0.1263	1.0945	-40.8528	38.0009	48.1291
5	8.0061	-3.6093	0.4299	2.4273	-0.3754	1.4706	0.4057	-0.6342	0.0742	-0.1674	-0.2234	-0.4625	0.1625	1.2071	-0.091	0.564	0.0699	0.1622	1.2155	0.2076	0.6068	-42.9196	32.935	49.4218
6	8.1892	-0.4866	0.2073	5.4129	1.059	2.5148	0.3411	-1.5371	1.0525	0.7605	-0.6679	-0.5703	-0.0027	0.731	0.2129	0.6652	0.1073	-0.0385	1.5746	0.5441	0.822	-31.0191	24.7177	49.9987
7	7.6584	0.8289	6.0606	6.3554	-0.3374	5.9963	-0.03	1.0667	-4.1758	1.4132	-0.7592	0.4978	1.9508	1.325	0.8852	0.8975	0.2096	0.5536	1.5107	0.2586	2.4798	-54.1901	11.6635	39.2319
8	1.6873	-0.1231	-1.0964	5.5559	-5.9125	8.4897	0.4409	-0.4965	0.2701	0.6356	-0.1611	-0.0129	-0.934	0.491	-0.2407	0.4327	-0.0245	0.1367	0.4332	0.0758	0.5345	-90.5472	61.1345	56.7768
9	3.5663	2.1244	-0.0373	6.6777	1.9101	3.4474	0.1082	-0.5751	-1.0819	-0.5874	0.5734	-1.4018	-0.0303	0.3219	0.6493	0.3107	-0.0666	0.1681	0.2157	0.155	0.4015	-82.8675	54.9164	56.0536
10	5.3942	1.3824	2.7192	2.5572	0.6226	3.1305	0.2941	1.1057	0.3791	-1.1063	-0.4108	-0.6863	-0.3188	0.8646	0.0038	0.4137	0.0232	0.2137	0.1319	0.0029	0.6279	-84.6344	55.158	44.3893
11	5.3929	-3.4133	-0.0196	5.232	-1.1833	0.7822	0.0167	-0.4675	1.2594	0.6185	0.4597	-0.7414	-0.8799	-0.2239	0.9979	-0.0251	-0.0724	0.3201	0.2765	0.1022	0.9138	-80.3625	60.7526	54.6687
12	5.1345	0.8673	2.1398	6.4988	0.8549	5.4086	0.473	1.1689	0.2243	-1.0261	-0.5363	0.7123	-0.412	0.9145	0.1052	0.3372	0.0724	0.0248	0.3536	0.0298	0.4492	-89.5245	59.8073	47.9923
13	4.0826	-4.4646	2.821	6.4838	-3.2425	2.0302	-0.1336	-0.0496	-0.1111	0.0314	-0.0596	-0.3686	-0.3062	-0.0084	0.1033	0.3563	0.0612	0.2212	0.4136	0.0521	0.4615	-93.6893	57.315	53.4712
14	4.1331	5.0462	-0.9732	7.6894	-3.7087	4.8283	-0.0127	0.6725	-1.2989	-1.2452	0.5188	-0.6417	0.5793	-0.7154	-0.1024	0.4356	-0.2175	0.112	0.5354	0.0364	0.6355	-130.5733	54.1033	45.1013
15	8.2445	3.2078	2.7257	6.5217	2.6508	3.4819	0.4057	0.5256	-0.0002	0.4775	0.0663	0.5736	0.4036	-0.3461	-0.3915	0.2853	0.0263	0.0207	0.2932	0.1764	0.3417	-117.264	62.7918	49.8363
16	3.5991	1.602	1.8817	6.4891	-1.243	1.7582	0.1514	-1.6777	0.569	1.1429	-0.1432	0.8599	-1.0752	-1.9372	-0.2052	0.4273	-0.0114	0.1235	0.9911	0.1015	0.3597	-128.6012	63.6167	58.8993
17	3.7278	3.9633	-4.8639	4.4913	-5.8533	7.9946	0.1878	0.5471	0.0187	-0.4541	0.2297	0.5958	-0.0619	-0.902	-0.1428	0.5292	-0.0081	0.0541	0.4059	-0.0307	0.4545	-112.1682	59.9073	49.3642
18	8.4801	2.1716	0.9686	3.5703	0.1193	6.4587	0.7525	-1.654	-1.4629	0.339	-0.2298	0.8358	0.6998	-0.9771	-0.2733	0.4384	-0.2017	0.0979	0.4908	0.1083	0.8602	-130.4071	53.4049	53.4979
19	8.4825	5.4678	1.484	6.0024	3.8814	6.5901	0.4947	-1.0327	-0.1111	0.5596	-0.2211	0.5328	-0.401	-1.5533	-0.1686	0.3515	-0.0424	0.0849	0.6525	0.2253	0.958	-132.8466	62.2511	54.8793
20	5.3543	4.5434	1.8708	7.8569	1.1957	4.7684	-0.1923	1.3861	0.9955	0.7749	0.0849	1.844	-0.0179	-1.0472	0.291	0.4262	0.0127	-0.009	0.6402	-0.0844	0.5656	-128.1535	68.586	50.3973
21	4.4096	4.4664	1.8245	7.6359	-0.5511	2.8623	0.1398	-0.0057	-0.6018	-0.0953	-0.2955	-0.1951	0.2312	0.299	0.2045	0.4114	0.045	0.0334	0.2289	0.0238	0.3265	-88.3232	36.6083	47.6027
22	4.0472	-3.4045	-2.4083	4.0873	4.5586	8.1408	0.1663	-0.1233	-0.0215	0.0374	0.2164	-0.2935	0.7741	-0.2433	-0.3398	0.5956	-0.0168	0.0487	0.2767	0.0758	0.6164	-85.2303	29.9279	53.1258
23	6.2064	-3.6409	0.9945	2.2915	-0.0525	0.426	0.1854	0.1733	0.2514	-0.208	-0.0955	-0.0404	0.0203	-0.105	-0.0279	0.5116	-0.0194	0.0706	0.2934	0.0037	0.231	-100.387	42.9617	45.9258
24	4.8805	-2.0101	1.7116	6.1674	-0.5768	0.5812	0.3298	-0.1285	-1.4577	-1.6496	0.0793	0.3301	0.9005	0.2698	-0.407	0.8148	0.1349	0.0358	0.3717	0.0588	0.9033	-117.5364	46.3894	41.4922
25	7.6007	-0.8621	0.4645	8.6972	0.8654	3.1476	0.7267	0.0364	-1.4505	0.5886	-0.173	-0.305	-0.2731	-0.2935	-0.3544	0.4818	-0.0003	-0.1043	0.3342	0.0705	0.5962	-116.0179	50.4548	45.3456
26	3.2074	-1.4474	1.166	1.0614	-1.554	3.543	0.0262	0.8219	-1.1087	-0.4633	0.1781	-0.6192	0.6922	0.3318	-0.1078	0.6029	0.1502	-0.0641	0.4998	-0.1074	0.8133	-123.2841	52.2616	33.6959
27	2.4715	-1.203	-1.4521	0.5858	0.7068	0.8511	-0.1753	-0.5504	-0.7772	0.5199	0.2607	-0.0976	-0.0435	0.4179	-0.0056	0.4798	0.5363	-0.2856	0.7436	0.068	0.8954	-141.5265	55.7125	40.0698

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 33 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 34 through 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 165 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 166 through 218 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 219 through 258 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 259 through 292 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 293 through 307 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 18 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 19 through 37 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 38 through 60 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 61 through 74 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 75 through 89 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 90 through 112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 113 through 127 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 128 through 143 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 144 through 154 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 155 through 173 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 174 through 185 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 186 through 196 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 197 through 213 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 15 through 53 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 54 through 74 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 75 through 146 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 147 through 164 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 165 through 187 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 188 through 221 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 222 through 224 )

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