[English] 日本語
![](img/lk-miru.gif)
- PDB-6jzh: Structure of human A2A adenosine receptor in complex with ZM24138... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6jzh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of human A2A adenosine receptor in complex with ZM241385 obtained from SFX experiments under atmospheric pressure | |||||||||
![]() | Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a | |||||||||
![]() | MEMBRANE PROTEIN / X-ray free-electron lasers room-temperature G-protein-coupled receptor | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Nango, E. / Shimamura, T. / Nakane, T. / Yamanaka, Y. / Mori, C. / Kimura, K.T. / Fujiwara, T. / Tanaka, T. / Iwata, S. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure. Authors: Shimazu, Y. / Tono, K. / Tanaka, T. / Yamanaka, Y. / Nakane, T. / Mori, C. / Terakado Kimura, K. / Fujiwara, T. / Sugahara, M. / Tanaka, R. / Doak, R.B. / Shimamura, T. / Iwata, S. / Nango, E. / Yabashi, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 180.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 4 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jziC ![]() 4eiyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
Experimental dataset #2 | Data reference: ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 49988.305 Da / Num. of mol.: 1 / Mutation: N154Q,M29W,H124I,R128L Source method: isolated from a genetically manipulated source Details: Chimera of Adenosine receptor A2a and Soluble cytochrome b562 Source: (gene. exp.) ![]() ![]() ![]() Production host: ![]() ![]() |
---|
-Non-polymers , 5 types, 90 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/ZMA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZMA.gif)
![](data/chem/img/OLA.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NA / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-ZMA / | ||||
#4: Chemical | ChemComp-OLA / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.01 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 27% (v/v) PEG400, 50-mM sodium thiocyanate, 2% (v/v) 2,5-hexanediol, 100-mM sodium citrate (pH 5.0) |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: May 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.9 Å / Num. obs: 25057 / % possible obs: 100 % / Redundancy: 139 % / CC1/2: 0.97 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.25→2.29 Å / CC1/2: 0.811 |
Serial crystallography sample delivery | Method: injection |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4EIY Resolution: 2.25→33.356 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.34
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→33.356 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|