[English] 日本語
Yorodumi
- PDB-8wdt: Crystal structure of the human adenosine A2A receptor in complex ... -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / 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 / Surfactant metabolism ...regulation of norepinephrine secretion / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / positive regulation of circadian sleep/wake cycle, sleep / 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 / Surfactant metabolism / sensory perception / positive regulation of urine volume / synaptic transmission, dopaminergic / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / synaptic transmission, cholinergic / positive regulation of glutamate secretion / intermediate filament / presynaptic active zone / blood circulation / response to caffeine / eating behavior / inhibitory postsynaptic potential / alpha-actinin binding / regulation of calcium ion transport / asymmetric synapse / axolemma / membrane depolarization / phagocytosis / cellular defense response / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / astrocyte activation / presynaptic modulation of chemical synaptic transmission / response to amphetamine / central nervous system development / positive regulation of long-term synaptic potentiation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / positive regulation of apoptotic signaling pathway / regulation of mitochondrial membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / apoptotic signaling pathway / locomotory behavior / negative regulation of inflammatory response / vasodilation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / 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 / calmodulin binding / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / dendrite / regulation of DNA-templated transcription / lipid binding / protein-containing complex binding / glutamatergic synapse / 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more