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Yorodumi- PDB-1yk0: structure of natriuretic peptide receptor-C complexed with atrial... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yk0 | |||||||||
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Title | structure of natriuretic peptide receptor-C complexed with atrial natriuretic peptide | |||||||||
Components | (Atrial natriuretic ...) x 2 | |||||||||
Keywords | HORMONE/GROWTH FACTOR RECEPTOR / HORMONE-RECEPTOR COMPLEX / NATRIURETIC PEPTIDE RECEPTOR / ALLOSTERIC ACTIVATION / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | |||||||||
Function / homology | Function and homology information positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / osteoclast proliferation / receptor guanylyl cyclase signaling pathway / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors ...positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / osteoclast proliferation / receptor guanylyl cyclase signaling pathway / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / 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 / negative regulation of JUN kinase activity / regulation of osteoblast proliferation / positive regulation of urine volume / sodium ion export across plasma membrane / neuropeptide hormone activity / G protein-coupled peptide receptor activity / cardiac muscle hypertrophy in response to stress / hormone receptor binding / negative regulation of systemic arterial blood pressure / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / chloride ion binding / positive regulation of heart rate / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / blood vessel remodeling / positive regulation of cardiac muscle contraction / response to muscle stretch / peptide binding / positive regulation of nitric-oxide synthase activity / skeletal system development / response to ischemia / cell projection / female pregnancy / regulation of blood pressure / vasodilation / hormone activity / protein folding / perikaryon / angiogenesis / collagen-containing extracellular matrix / Amyloid fiber formation / signaling receptor binding / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | He, X. / Garcia, K.C. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural determinants of natriuretic peptide receptor specificity and degeneracy. Authors: He, X.L. / Dukkipati, A. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yk0.cif.gz | 333.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yk0.ent.gz | 272.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yk0_validation.pdf.gz | 1013.1 KB | Display | wwPDB validaton report |
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Full document | 1yk0_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1yk0_validation.xml.gz | 72.2 KB | Display | |
Data in CIF | 1yk0_validation.cif.gz | 99.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1yk0 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1yk0 | HTTPS FTP |
-Related structure data
Related structure data | 1yk1C 1jdpS C: citing same article (ref.) S: Starting model for refinement |
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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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Number of models | 2 |
-Components
-Atrial natriuretic ... , 2 types, 3 molecules ABE
#1: Protein | Mass: 52904.695 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPR3, ANPRC / Plasmid: PRMHA3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P17342 #2: Protein/peptide | | Mass: 2165.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P01160 |
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-Sugars , 2 types, 4 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#4: Sugar |
-Non-polymers , 2 types, 322 molecules
#5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JDP Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å /
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