[English] 日本語
Yorodumi
- PDB-8rwx: Steady state structure of the human adenosine A2A receptor bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rwx
TitleSteady state structure of the human adenosine A2A receptor bound to synthetic photoswitch 'StilSwitch3' determined by serial synchrotron crystallography
ComponentsAdenosine receptor A2a,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / adenosine receptor / synthetic photoswitch / Parkinson's disease
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 / electron transport chain / 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 / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / iron ion binding / response to xenobiotic stimulus / inflammatory response / negative regulation of cell population proliferation / neuronal cell body / heme binding / 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 / 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
: / OLEIC ACID / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsGlover, H. / Bertrand, Q. / Weinert, T.
Funding support Switzerland, Germany, 7items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_207462 Switzerland
Swiss National Science Foundation310030_197674 Switzerland
Swiss National Science FoundationCRSII4_213507 Switzerland
Other government42711.1 IP-LS
Swiss Nanoscience Institute#1904 Switzerland
German Research Foundation (DFG)1850/4-3 Germany
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2024
Title: Photoswitch dissociation from a G protein-coupled receptor resolved by time-resolved serial crystallography.
Authors: Glover, H. / Sassmannshausen, T. / Bertrand, Q. / Trabuco, M. / Slavov, C. / Bacchin, A. / Andres, F. / Kondo, Y. / Stipp, R. / Wranik, M. / Khusainov, G. / Carrillo, M. / Kekilli, D. / Nan, ...Authors: Glover, H. / Sassmannshausen, T. / Bertrand, Q. / Trabuco, M. / Slavov, C. / Bacchin, A. / Andres, F. / Kondo, Y. / Stipp, R. / Wranik, M. / Khusainov, G. / Carrillo, M. / Kekilli, D. / Nan, J. / Gonzalez, A. / Cheng, R. / Neidhart, W. / Weinert, T. / Leonarski, F. / Dworkowski, F. / Kepa, M. / Wachtveitl, J. / Hennig, M. / Standfuss, J.
History
DepositionFeb 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,74219
Polymers49,8291
Non-polymers4,91318
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint31 kcal/mol
Surface area20850 Å2
Unit cell
Length a, b, c (Å)40.550, 182.540, 143.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 49829.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 ...Details: A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.,A2A-StaR2-bRIL562 construct (A2A with bRIL insertion), with A277S revert mutation.
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
#2: Chemical ChemComp-A1H3H / 1,3-diethyl-8-[(~{E})-2-(4-methoxy-3-oxidanyl-phenyl)ethenyl]-7-methyl-purine-2,6-dione


Mass: 370.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C18H34O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 % / Description: Square plates
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.85
Details: 0.1 M sodium potassium phosphate pH 5.85, 27-30% PEG 500 MME, 0.2 M sodium thiocyanate, 0.4 mM StilSwitch3

-
Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→142.13 Å / Num. obs: 10568 / % possible obs: 100 % / Redundancy: 252.2 % / CC1/2: 0.992 / CC star: 0.998 / R split: 0.1432 / Net I/σ(I): 5.11
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 151.6 % / Mean I/σ(I) obs: 0.61 / Num. unique obs: 993 / CC1/2: 0.216 / CC star: 0.596 / R split: 1.6113 / % possible all: 100
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: LCP / Injector temperature: 293 K / Jet diameter: 75 µm
Serial crystallography data reductionFrames indexed: 20578

-
Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHENIX1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→19.94 Å / SU ML: 0.82 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 42.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.347 529 5.01 %
Rwork0.3103 --
obs0.312 10568 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 239 0 3164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023219
X-RAY DIFFRACTIONf_angle_d0.4574327
X-RAY DIFFRACTIONf_dihedral_angle_d8.536588
X-RAY DIFFRACTIONf_chiral_restr0.034494
X-RAY DIFFRACTIONf_plane_restr0.003552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.360.46151290.44392461X-RAY DIFFRACTION100
3.36-3.840.42231300.36172458X-RAY DIFFRACTION100
3.84-4.820.31581320.28952511X-RAY DIFFRACTION100
4.82-19.940.31081380.27662609X-RAY DIFFRACTION100

+
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