[English] 日本語
Yorodumi
- PDB-3uzc: Thermostabilised Adenosine A2A receptor in complex with 4-(3-amin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / 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 / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / 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 / prepulse inhibition / cellular defense response / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / astrocyte activation / locomotory behavior / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / negative regulation of neuron apoptotic process / postsynaptic membrane / calmodulin binding / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / apoptotic process / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / 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-T4E / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.341 Å
AuthorsCongreve, M. / Andrews, S.P. / Dore, A.S. / Hollenstein, K. / Hurrell, E. / Langmead, C.J. / Mason, J.S. / Ng, I.W. / 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine A2A Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7782
Polymers36,4791
Non-polymers2991
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.700, 112.064, 126.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein 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-T4E / 4-(3-amino-5-phenyl-1,2,4-triazin-6-yl)-2-chlorophenol


Mass: 298.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClN4O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 5.39 Å3/Da / Density % sol: 77.2 %
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, 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: 3.34→49.29 Å / Num. all: 10975 / Num. obs: 10975 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8
Reflection shellResolution: 3.34→3.52 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1611 / % possible all: 96.1

-
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

3pwh


Resolution: 3.341→19.805 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 1.36 / Phase error: 39.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2899 511 4.73 %RANDOM
Rwork0.2822 ---
obs0.2825 10797 92.2 %-
all-10797 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.799 Å2 / ksol: 0.225 e/Å3
Displacement parametersBiso max: 389.77 Å2 / Biso mean: 155.9 Å2 / Biso min: 74.21 Å2
Baniso -1Baniso -2Baniso -3
1-19.3024 Å2-0 Å20 Å2
2---61.7626 Å2-0 Å2
3---42.4601 Å2
Refinement stepCycle: LAST / Resolution: 3.341→19.805 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_d0.3923180
X-RAY DIFFRACTIONf_chiral_restr0.027377
X-RAY DIFFRACTIONf_plane_restr0.002390
X-RAY DIFFRACTIONf_dihedral_angle_d11.047789
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 (%)
3.3413-3.67560.47631280.43282531265993
3.6756-4.2030.39241320.31122544267692
4.203-5.27870.2291130.2422603271693
5.2787-19.80490.23551380.25662608274691
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)
10.78220.4622-0.23050.3730.33271.8361-0.1385-0.8816-0.25940.93290.89120.01890.0662-0.621-01.0231-0.0170.07980.70210.06192.047319.896126.422342.3237
20.0116-0.017-0.00730.01370.0043-0.0001-0.33010.47471.05370.0858-0.2420.16530.11670.94601.66750.25780.14131.0670.00192.913120.892344.570830.339
30.0143-0.1838-0.26030.58070.82841.1947-0.9074-0.3434-0.0174-1.3947-0.0631-0.34870.8982-0.2434-01.15420.01860.52040.79710.18421.509517.609522.70334.0599
40.23090.0122-0.10180.11030.04280.06420.01150.8587-0.2868-0.89140.66360.0630.70.11820.00021.7182-0.48130.30041.41880.2643.26777.55854.244732.5211
50.4029-0.02320.53580.0441-0.14340.5634-0.18281.1155-0.2695-1.68560.8480.4586-0.0157-0.807900.9384-0.18080.260.93720.28332.041721.167323.390924.3474
60.13360.10020.1680.07850.13430.2243-0.86821.28550.6853-1.3287-0.13640.630.51420.170101.77620.08740.41490.75030.09392.656226.381343.440214.5747
70.8191-0.29080.28330.1084-0.04510.4180.52491.6907-0.5014-1.48770.49020.97950.4425-0.30601.025-0.0383-0.42250.7615-0.05961.851813.984923.335920.1521
80.1094-0.01240.08270.01330.0190.12080.23060.7374-0.139-0.2607-0.3527-0.12460.2734-1.0394-0.00021.62940.1160.10541.29590.02332.756713.5006-0.273522.2445
90.0866-0.13820.12490.40350.06160.52611.4071-0.1516-0.4675-1.73580.19611.1981.5934-0.3512-01.447-0.0032-0.04090.86820.00412.538813.29240.398230.1014
100.9021-0.8373-0.28240.74750.12510.3133-0.32840.171.392-0.0231-0.2569-0.5113-0.00530.0241-01.4013-0.26410.08590.87820.17842.175833.910425.924517.8107
110.0374-0.01810.0850.0068-0.03920.19110.4686-0.19360.1141-0.32920.7021-0.66290.9089-0.205701.8685-0.08620.75431.31270.50883.269344.99154.165218.5103
121.87110.1736-1.24050.4612-0.61131.123-0.58010.7994-0.7424-1.2941.576-2.6155-0.7585-0.21220.00011.1445-0.0516-0.18050.9679-0.00391.160133.613324.788726.7588
130.2831-0.02220.22080.0883-0.00380.146-0.0784-0.7130.7774-0.930.95180.3694-0.78160.711801.094-0.12920.05930.78690.01283.320732.4025-2.097730.1301
14-0.0895-0.05420.10880.4893-0.32011.7409-0.1174-0.94650.14480.919-0.1173-0.4923-0.61540.61931.34190.23230.0443-1.33960.8151-0.2153-1.486629.338721.900937.3562
150.129-0.0107-0.0480.0934-0.12170.1179-0.3614-0.53411.15451.6046-0.0558-1.0137-2.27351.73301.0979-0.0171-0.34060.8537-0.00221.82125.927742.785642.7276
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