[English] 日本語
Yorodumi
- PDB-3uza: Thermostabilised Adenosine A2A receptor in complex with 6-(2,6-Di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uza
TitleThermostabilised Adenosine A2A receptor in complex with 6-(2,6-Dimethylpyridin-4-yl)-5-phenyl-1,2,4-triazin-3-amine
ComponentsAdenosine receptor A2aAdenosine A2A receptor
KeywordsSIGNALING PROTEIN / 7TM / GPCR / G-PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / synaptic transmission, dopaminergic / response to purine-containing compound / sensory perception ...positive regulation of acetylcholine secretion, neurotransmission / regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / Adenosine P1 receptors / negative regulation of alpha-beta T cell activation / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / synaptic transmission, dopaminergic / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / protein kinase C-activating G protein-coupled receptor signaling pathway / synaptic transmission, cholinergic / inhibitory postsynaptic potential / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / intermediate filament / response to caffeine / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / response to inorganic substance / axolemma / asymmetric synapse / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / positive regulation of apoptotic signaling pathway / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / locomotory behavior / central nervous system development / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / astrocyte activation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / 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 / dendrite / lipid binding / glutamatergic synapse / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-T4G / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.273 Å
AuthorsCongreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / Tehan, B. / Zhukov, A. ...Congreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / Tehan, B. / Zhukov, A. / Weir, M. / Marshall, F.H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of 1,2,4-Triazine Derivatives as Adenosine A(2A) Antagonists using Structure Based Drug Design
Authors: Congreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / Tehan, B. / Zhukov, A. / Weir, M. / Marshall, F.H.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7562
Polymers36,4791
Non-polymers2771
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.814, 111.896, 125.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Adenosine receptor A2a / Adenosine A2A receptor


Mass: 36479.102 Da / Num. of mol.: 1 / Fragment: residues 1-317 / Mutation: A54L T88A R107A K122A L202A L235A V239A S277A
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: Chemical ChemComp-T4G / 6-(2,6-dimethylpyridin-4-yl)-5-phenyl-1,2,4-triazin-3-amine


Mass: 277.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N5

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 5.395047 Å3/Da / Density % sol: 77.201309 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32-42% PEG1000, 0.25M MGCL2, 0.3% NG, 0.1%(W/V) 1-BUTANOL, 0.05% CYMAL-6, 0.1M TRIS-HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2010
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 3.273→49.4 Å / Num. all: 11568 / Num. obs: 11568 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 94.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 3.273→3.46 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1566 / % possible all: 88.2

-
Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.4_84)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWH
Resolution: 3.273→19.773 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 0.51 / Phase error: 42.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3347 548 4.81 %RANDOM
Rwork0.2932 ---
obs0.2952 11401 91.57 %-
all-11401 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.161 Å2 / ksol: 0.22 e/Å3
Displacement parametersBiso max: 298.15 Å2 / Biso mean: 154.8989 Å2 / Biso min: 67.59 Å2
Baniso -1Baniso -2Baniso -3
1--72.3092 Å2-0 Å20 Å2
2--7.0546 Å2-0 Å2
3---45.6694 Å2
Refinement stepCycle: LAST / Resolution: 3.273→19.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 21 0 2271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022333
X-RAY DIFFRACTIONf_angle_d0.4663180
X-RAY DIFFRACTIONf_chiral_restr0.031377
X-RAY DIFFRACTIONf_plane_restr0.002390
X-RAY DIFFRACTIONf_dihedral_angle_d11.809789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2726-3.60020.4261180.3952599271788
3.6002-4.1170.39341580.33162703286194
4.117-5.17160.29661360.26072736287293
5.1716-19.77380.30741360.26382815295192
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.573-0.4859-1.29810.69370.73333.38591.5321-0.4203-1.14290.99760.2253-0.08870.577-0.186200.7974-0.0532-0.19111.05420.08912.253429.860119.878741.9416
20.02860.02310.02680.02250.03210.04380.40981.6802-0.2703-1.7773-0.02950.71180.72851.241501.02640.06090.0491.4670.36442.703611.691821.22829.8354
30.57880.2259-0.69520.7159-0.09230.90070.00761.18040.88420.3159-0.6586-1.0298-0.05110.1067-00.84030.061-0.3570.91010.42262.366933.554617.756433.5287
40.1244-0.08540.00670.4084-0.21170.1322-0.0765-0.15890.3099-1.22460.1678-0.4967-0.88821.05360.00010.71630.3037-0.07331.09930.18593.322951.88957.670331.7134
50.29770.18650.03560.43110.59911.00821.42280.9274-0.4301-1.5677-0.1297-0.11541.3687-0.1525-01.00130.3537-0.21940.84430.48231.099232.824321.618223.9034
60.1467-0.1602-0.19240.18250.21120.2377-0.25072.0818-0.5415-2.182-0.15030.26940.59720.989901.0868-0.0266-0.19591.90580.45453.531912.854727.173114.2424
70.12480.1442-0.10950.65090.47130.81490.48542.2377-0.3539-1.70630.0087-0.75880.52350.6693-01.20260.039-0.24141.4771-0.12812.140332.888114.60519.5265
80.01510.04740.01750.26130.17710.151-2.56380.1327-0.4075-1.5054-0.03110.49752.55040.7844-0.00021.3244-0.24370.15191.35390.13643.643456.542713.955721.6676
90.4984-0.178-0.2810.69210.85971.07691.42551.7188-0.1189-0.88740.4692-0.87771.19282.178200.96510.0355-0.22681.4727-0.17993.104655.80413.4629.5073
100.77460.83540.44270.90380.24861.8450.0479-0.69060.75350.0033-0.20910.41720.2613-0.219700.89170.2854-0.16351.31730.19181.680630.386434.614117.7844
110.041-0.0084-0.06770.00340.01670.11-0.73671.31590.4136-0.611.4132-0.2355-0.71381.069801.1082-0.0152-0.44061.60250.52013.47132.223745.738218.7634
120.4526-0.02720.92061.8293-1.14232.38941.53040.97971.9018-1.1397-0.4916-0.46690.1125-0.48650.00010.84410.0149-0.04330.6548-0.1771.784331.488333.980626.7093
130.35720.20180.0750.41960.47690.64871.53422.2205-0.4853-0.0984-1.70011.2596-1.0689-0.45210.00110.93640.113-0.18161.1418-0.03472.773758.320132.621430.1614
140.3439-0.06560.24720.14610.59521.68670.0402-0.5240.24770.1374-0.1282-0.2133-0.3508-0.62760.59791.0619-0.13170.19120.1901-1.2089-0.629234.46829.229737.1336
150.15630.21010.0870.39440.11070.04080.3952-0.89740.22060.0266-0.12581.8021-1.7608-3.0972-01.11350.032-0.0761.8098-0.16462.067413.531725.89142.3899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 7:33A7 - 33
2X-RAY DIFFRACTION2chain A and resid 34:40A34 - 40
3X-RAY DIFFRACTION3chain A and resid 41:68A41 - 68
4X-RAY DIFFRACTION4chain A and resid 69:76A69 - 76
5X-RAY DIFFRACTION5chain A and resid 77:104A77 - 104
6X-RAY DIFFRACTION6chain A and resid 105:118A105 - 118
7X-RAY DIFFRACTION7chain A and resid 119:141A119 - 141
8X-RAY DIFFRACTION8chain A and resid 142:149A142 - 149
9X-RAY DIFFRACTION9chain A and resid 158:175A158 - 175
10X-RAY DIFFRACTION10chain A and resid 176:211A176 - 211
11X-RAY DIFFRACTION11chain A and resid 212:220A212 - 220
12X-RAY DIFFRACTION12chain A and resid 221:258A221 - 258
13X-RAY DIFFRACTION13chain A and resid 259:267A259 - 267
14X-RAY DIFFRACTION14chain A and resid 268:292A268 - 292
15X-RAY DIFFRACTION15chain A and resid 293:305A293 - 305

+
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