[English] 日本語
![](img/lk-miru.gif)
- PDB-7brk: Atrial Natriuretic Peptide Receptor complexed with deletion mutan... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7brk | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Atrial Natriuretic Peptide Receptor complexed with deletion mutant of human Atrial Natriuretic Peptide[5-27] | |||||||||
![]() |
| |||||||||
![]() | MEMBRANE PROTEIN / RECEPTOR-HORMONE COMPLEX / NATRIURETIC PEPTIDE / NATRIURETIC PEPTIDE RECEPTOR / GUANYLYL-CYCLASE-COUPLED RECEPTOR / SIGNAL TRANSMISSION / ROTATION MECHANISM / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() Physiological factors / positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / guanylate cyclase ...Physiological factors / positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / guanylate cyclase / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / guanylate cyclase activity / Physiological factors / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hormone binding / negative regulation of JUN kinase activity / sodium ion export across plasma membrane / neuropeptide hormone activity / cardiac muscle hypertrophy in response to stress / negative regulation of systemic arterial blood pressure / hormone receptor binding / aortic valve morphogenesis / adenylate cyclase activity / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / response to muscle stretch / blood vessel diameter maintenance / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / hormone activity / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / Amyloid fiber formation / signaling receptor binding / GTP binding / protein-containing complex / extracellular space / extracellular region / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ogawa, H. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural insight into hormone-recognition and transmembrane signaling by the atrial natriuretic peptide receptor Authors: Ogawa, H. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 378.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 312.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 47.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7brgC ![]() 7brhC ![]() 7briC ![]() 7brjC ![]() 7brlC ![]() 1dp4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Protein/peptide , 2 types, 3 molecules ABL
#1: Protein | Mass: 48434.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | | Mass: 2409.708 Da / Num. of mol.: 1 / Mutation: deletions of residues 1-4 and 28 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|
-Sugars , 2 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 2 types, 112 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.04 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, MES / PH range: 6.3 - 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Aug 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 30557 / % possible obs: 90.2 % / Redundancy: 15.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2.85→2.93 Å / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2829 / CC1/2: 0.55 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DP4 Resolution: 2.85→43.106 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 26.76
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→43.106 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|