[English] 日本語
![](img/lk-miru.gif)
- PDB-8a2p: Room-temperature structure of the stabilised A2A-LUAA47070 comple... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8a2p | ||||||
---|---|---|---|---|---|---|---|
Title | Room-temperature structure of the stabilised A2A-LUAA47070 complex determined by synchrotron serial crystallography | ||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562 | ||||||
![]() | MEMBRANE PROTEIN / Adenosine receptor A2a / Soluble cytochrome b562 | ||||||
Function / homology | ![]() positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / positive regulation of urine volume / NGF-independant TRKA activation / Surfactant metabolism / synaptic transmission, dopaminergic / : / inhibitory postsynaptic potential / negative regulation of vascular permeability / synaptic transmission, cholinergic / type 5 metabotropic glutamate receptor binding / positive regulation of glutamate secretion / blood circulation / response to caffeine / intermediate filament / eating behavior / presynaptic active zone / alpha-actinin binding / membrane depolarization / regulation of calcium ion transport / asymmetric synapse / axolemma / : / cellular defense response / prepulse inhibition / phagocytosis / response to amphetamine / presynaptic modulation of chemical synaptic transmission / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / synaptic transmission, glutamatergic / positive regulation of long-term synaptic potentiation / locomotory behavior / central nervous system development / astrocyte activation / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / apoptotic signaling pathway / electron transport chain / positive regulation of apoptotic signaling pathway / 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 / periplasmic space / electron transfer activity / calmodulin binding / response to xenobiotic stimulus / inflammatory response / iron ion binding / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / lipid binding / apoptotic process / dendrite / heme binding / protein-containing complex binding / regulation of DNA-templated transcription / enzyme binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moraes, I. / Kwan, T.O.C. / Axford, D. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / ...Authors: Birch, J. / Kwan, T.O.C. / Judge, P.J. / Axford, D. / Aller, P. / Butryn, A. / Reis, R.I. / Bada Juarez, J.F. / Vinals, J. / Owen, R.L. / Nango, E. / Tanaka, R. / Tono, K. / Joti, Y. / Tanaka, T. / Owada, S. / Sugahara, M. / Iwata, S. / Orville, A.M. / Watts, A. / Moraes, I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 175.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 137.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zy3C ![]() 8a2oC ![]() 5olvS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46929.750 Da / Num. of mol.: 1 Mutation: A54L,T88A,R107A,K122A,L202A,L235A,V239A6,S277A,N154A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 21 molecules ![](data/chem/img/9Y2.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-9Y2 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-OLA / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.92 % / Description: plates |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.5 Details: 0.1 M tri-sodium citrate pH 4.5, 0.05 M sodium thiocyanate, 29% (v/v) polyethylene glycol 400, 2% (v/v) 2,5-hexanediol PH range: 4.0-5.5 / Temp details: constant |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→90.93 Å / Num. obs: 7126 / % possible obs: 99.6 % / Redundancy: 88.9 % / Biso Wilson estimate: 84.1 Å2 / CC1/2: 0.973 / R split: 0.22 / Net I/σ(I): 13.68 |
Reflection shell | Resolution: 3.5→3.56 Å / Redundancy: 36 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 344 / CC1/2: 0.595 / R split: 0.641 / % possible all: 100 |
Serial crystallography sample delivery | Description: LCP injector / Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: LCP / Flow rate: 8 µL/min / Injector nozzle: gas / Injector temperature: 293 K / Jet diameter: 50 µm / Preparation: High density crystals |
Serial crystallography data reduction | Frames indexed: 3618 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5OLV Resolution: 3.5→90.92 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.905 / SU B: 57.019 / SU ML: 0.394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.632 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 220.29 Å2 / Biso mean: 118.027 Å2 / Biso min: 61.09 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→90.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -16.851 Å / Origin y: -17.252 Å / Origin z: 18.662 Å
|