[English] 日本語
![](img/lk-miru.gif)
- PDB-7xka: Structure of human beta2 adrenergic receptor bound to constrained... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7xka | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of human beta2 adrenergic receptor bound to constrained epinephrine | ||||||
![]() |
| ||||||
![]() | MEMBRANE PROTEIN / GPCR | ||||||
Function / homology | ![]() : / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure ...: / beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / positive regulation of AMPA receptor activity / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / positive regulation of bone mineralization / brown fat cell differentiation / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of sodium ion transport / viral release from host cell by cytolysis / bone resorption / activation of adenylate cyclase activity / response to cold / peptidoglycan catabolic process / receptor-mediated endocytosis / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein serine/threonine kinase activity / cellular response to amyloid-beta / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / host cell cytoplasm / transcription by RNA polymerase II / positive regulation of MAPK cascade / cell surface receptor signaling pathway / lysosome / early endosome / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / defense response to bacterium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. ...Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M. / Stobel, A. / Maul, L. / Mayer, D. / Hubner, H. / Venkatakrishnan, A. / Dror, R. / Kobilka, B.K. / Sunahara, R. / Liu, X. / Gmeiner, P. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Constrained catecholamines gain beta 2 AR selectivity through allosteric effects on pocket dynamics. Authors: Xu, X. / Shonberg, J. / Kaindl, J. / Clark, M.J. / Stossel, A. / Maul, L. / Mayer, D. / Hubner, H. / Hirata, K. / Venkatakrishnan, A.J. / Dror, R.O. / Kobilka, B.K. / Sunahara, R.K. / Liu, X. / Gmeiner, P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 140.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 719.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 722.7 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xk9C ![]() 4ldeS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53471.039 Da / Num. of mol.: 1 / Mutation: C918T,C962A,M1096T,M1098T,N1157E,C1265A Source method: isolated from a genetically manipulated source Details: Chimera protein Source: (gene. exp.) Enterobacteria phage T4, (gene. exp.) ![]() Gene: ADRB2, ADRB2R, B2AR / Production host: ![]() ![]() |
---|---|
#2: Antibody | Mass: 12949.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-G1I / ( |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.21 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 100mM Tris-HCl, pH 8.0, 150-200mM lithium acetate, 43-45% PEG400 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→19.96 Å / Num. obs: 18898 / % possible obs: 98.96 % / Redundancy: 11.3 % / Biso Wilson estimate: 66.45 Å2 / CC1/2: 0.983 / Net I/σ(I): 6.73 |
Reflection shell | Resolution: 3.1→3.2 Å / Num. unique obs: 1618 / CC1/2: 0.598 / % possible all: 97.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 4LDE Resolution: 3.1→19.96 Å / SU ML: 0.5325 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5997 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→19.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|