[English] 日本語
Yorodumi
- PDB-5olg: Structure of the A2A-StaR2-bRIL562-ZM241385 complex at 1.86A obta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5olg
TitleStructure of the A2A-StaR2-bRIL562-ZM241385 complex at 1.86A obtained from in meso soaking experiments.
ComponentsAdenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
KeywordsMEMBRANE PROTEIN / G-Protein Coupled Receptor / Adenosine 2a receptor / 7 TM integral membrane protein / thermostabilizing mutations / membrane proteins
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / 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 / regulation of norepinephrine secretion / synaptic transmission, dopaminergic / response to purine-containing compound / sensory perception ...positive regulation of acetylcholine secretion, neurotransmission / 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 / regulation of norepinephrine secretion / synaptic transmission, dopaminergic / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, cholinergic / protein kinase C-activating G protein-coupled receptor signaling pathway / 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 / regulation of calcium ion transport / membrane depolarization / response to inorganic substance / asymmetric synapse / axolemma / positive regulation of synaptic transmission, glutamatergic / cellular defense response / prepulse inhibition / neuron projection morphogenesis / phagocytosis / response to amphetamine / positive regulation of apoptotic signaling pathway / excitatory postsynaptic potential / astrocyte activation / presynaptic modulation of chemical synaptic transmission / regulation of mitochondrial membrane potential / locomotory behavior / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / synaptic transmission, glutamatergic / central nervous system development / positive regulation of long-term synaptic potentiation / apoptotic signaling pathway / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / vasodilation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / electron transfer activity / calmodulin binding / periplasmic space / inflammatory response / response to xenobiotic stimulus / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / dendrite / lipid binding / glutamatergic synapse / protein-containing complex binding / apoptotic process / heme binding / regulation of DNA-templated transcription / enzyme binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
CITRIC ACID / CHOLESTEROL / OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / THIOCYANATE ION / Chem-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsRucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R. / Marshall, F.H. / Dore, A.S.
Funding support1items
OrganizationGrant numberCountry
European Union115366
CitationJournal: Sci Rep / Year: 2018
Title: Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A2A Receptor crystals.
Authors: Rucktooa, P. / Cheng, R.K.Y. / Segala, E. / Geng, T. / Errey, J.C. / Brown, G.A. / Cooke, R.M. / Marshall, F.H. / Dore, A.S.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_refine_tls_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,27132
Polymers48,0681
Non-polymers8,20331
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric peak on size exclusion chromatography.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint26 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.450, 179.393, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a / Cytochrome b-562


Mass: 48067.824 Da / Num. of mol.: 1
Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; ...Mutation: A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A,A54L; T88A; R107A; K122A; L202A; L235A; V239A; S277A; N154A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P29274, UniProt: P0ABE7

-
Non-polymers , 8 types, 119 molecules

#2: Chemical ChemComp-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol / ZM-241,385


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#3: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#7: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 % / Description: 0.060-0.080 mm long plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol, 0.5 mM theophylline. ZM241385 was subsequently added to motherliquor ...Details: Crystal growth: 0.l M tri-sodium citrate pH 5.3-5.4, 0.05 M sodium thiocyanate, 29-32% PEG400, 2% (v/v) 2,5-hexanediol, 0.5 mM theophylline. ZM241385 was subsequently added to motherliquor for the soaking experiment at a final concentration of 0.005 mM.
PH range: 5.3-5.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→46.53 Å / Num. obs: 42870 / % possible obs: 98.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.7
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.197 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.12RC2_2821)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZJ

5mzj


Resolution: 1.87→41.31 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.67
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3894 5 %Random
Rwork0.189 ---
obs0.191 41376 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.73 Å2
Refinement stepCycle: LAST / Resolution: 1.87→41.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 534 88 3636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123703
X-RAY DIFFRACTIONf_angle_d1.4474946
X-RAY DIFFRACTIONf_dihedral_angle_d16.6172276
X-RAY DIFFRACTIONf_chiral_restr0.07551
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shellResolution: 1.865→1.932 Å
RfactorNum. reflection% reflection
Rfree0.5144 200 -
Rwork0.4834 3701 -
obs--100 %
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)
10.67590.09550.19730.66910.01230.82080.0198-0.0048-0.0381-0.0743-0.0088-0.0320.0917-0.0559-00.1778-0.00240.00310.18590.00640.1615-22.1678-7.056317.6583
20.077-0.0034-0.07210.1943-0.09530.21070.0456-0.26580.3529-0.29420.0507-0.15410.15640.10430.00070.40540.0712-0.01240.3022-0.02610.67490.1168-54.561119.9519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A'A-1 - 305
2X-RAY DIFFRACTION2CHAIN 'A'A1001 - 1106

+
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