[English] 日本語
![](img/lk-miru.gif)
- PDB-6do1: Structure of nanobody-stabilized angiotensin II type 1 receptor b... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6do1 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8 | |||||||||||||||||||||
![]() |
| |||||||||||||||||||||
![]() | MEMBRANE PROTEIN / nanobody / GPCR / synthetic antibody | |||||||||||||||||||||
Function / homology | ![]() angiotensin type I receptor activity / positive regulation of phospholipase A2 activity / angiotensin type II receptor activity / phospholipase C-activating angiotensin-activated signaling pathway / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of macrophage derived foam cell differentiation ...angiotensin type I receptor activity / positive regulation of phospholipase A2 activity / angiotensin type II receptor activity / phospholipase C-activating angiotensin-activated signaling pathway / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of CoA-transferase activity / low-density lipoprotein particle remodeling / regulation of systemic arterial blood pressure by renin-angiotensin / Rho protein signal transduction / regulation of vasoconstriction / positive regulation of protein metabolic process / blood vessel diameter maintenance / Peptide ligand-binding receptors / cell chemotaxis / kidney development / angiotensin-activated signaling pathway / regulation of cell growth / electron transport chain / calcium-mediated signaling / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / G alpha (q) signalling events / periplasmic space / electron transfer activity / inflammatory response / symbiont entry into host cell / iron ion binding / G protein-coupled receptor signaling pathway / protein heterodimerization activity / heme binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Wingler, L.M. / McMahon, C. / Staus, D.P. / Lefkowitz, R.J. / Kruse, A.C. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody. Authors: Wingler, L.M. / McMahon, C. / Staus, D.P. / Lefkowitz, R.J. / Kruse, A.C. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 218.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 168.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein / Antibody / Protein/peptide / Sugars , 4 types, 10 molecules ABCDEFGH![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 48514.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B, cybC / Cell line (production host): Expi293F / Production host: ![]() #2: Antibody | Mass: 13711.979 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Protein/peptide | Mass: 970.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Sugar | |
---|
-Non-polymers , 3 types, 86 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OLC.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-OLC / ( #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: lipidic cubic phase / pH: 8 Details: Protein was reconstituted with a 10:1 (w:w) mix of monoolein and cholesterol. Crystals were grown in cubic phase sandwich plates with using 100 mM Tris pH 8.0, 15-25 mM MgCl2, and 28-29% PEG 300 |
-Data collection
Diffraction | Mean temperature: 80 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→45.6 Å / Num. obs: 29111 / % possible obs: 98.5 % / Redundancy: 3.6 % / CC1/2: 0.962 / Rrim(I) all: 0.41 / Χ2: 0.96 / Net I/σ(I): 2.1 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.457 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4662 / CC1/2: 0.562 / Rrim(I) all: 1.697 / Χ2: 0.98 / % possible all: 99.3 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4YAY, 3P0G Resolution: 2.901→43.618 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.04 / Stereochemistry target values: LS_WUNIT_K1
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.901→43.618 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|