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Yorodumi- PDB-7brk: Atrial Natriuretic Peptide Receptor complexed with deletion mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7brk | |||||||||
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Title | Atrial Natriuretic Peptide Receptor complexed with deletion mutant of human Atrial Natriuretic Peptide[5-27] | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / RECEPTOR-HORMONE COMPLEX / NATRIURETIC PEPTIDE / NATRIURETIC PEPTIDE RECEPTOR / GUANYLYL-CYCLASE-COUPLED RECEPTOR / SIGNAL TRANSMISSION / ROTATION MECHANISM / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / guanylate cyclase / regulation of high voltage-gated calcium channel activity ...ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / guanylate cyclase / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / guanylate cyclase activity / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / hormone binding / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / sodium ion export across plasma membrane / negative regulation of JUN kinase activity / neuropeptide hormone activity / negative regulation of systemic arterial blood pressure / cardiac muscle hypertrophy in response to stress / adenylate cyclase activity / hormone receptor binding / aortic valve morphogenesis / 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 | Rattus norvegicus (Norway rat) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Ogawa, H. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: Structural insight into hormone-recognition and transmembrane signaling by the atrial natriuretic peptide receptor Authors: Ogawa, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7brk.cif.gz | 378.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7brk.ent.gz | 312.9 KB | Display | PDB format |
PDBx/mmJSON format | 7brk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7brk ftp://data.pdbj.org/pub/pdb/validation_reports/br/7brk | HTTPS FTP |
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-Related structure data
Related structure data | 7brgC 7brhC 7briC 7brjC 7brlC 1dp4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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.) Rattus norvegicus (Norway rat) / Gene: Npr1 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P18910, guanylate cyclase #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.) Homo sapiens (human) / References: UniProt: P01160 |
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-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 |
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-Non-polymers , 2 types, 112 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67.04 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→43.106 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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