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Yorodumi- PDB-1yk1: structure of natriuretic peptide receptor-C complexed with brain ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yk1 | |||||||||
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Title | structure of natriuretic peptide receptor-C complexed with brain natriuretic peptide | |||||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR RECEPTOR / HORMONE-RECEPTOR COMPLEX / NATRIURETIC PEPTIDE RECEPTOR / ALLOSTERIC ACTIVATION / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX | |||||||||
Function / homology | Function and homology information diuretic hormone activity / natriuretic peptide receptor activity / osteoclast proliferation / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / cGMP biosynthetic process / regulation of vascular permeability / cardiac conduction system development / hormone binding ...diuretic hormone activity / natriuretic peptide receptor activity / osteoclast proliferation / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / cGMP biosynthetic process / regulation of vascular permeability / cardiac conduction system development / hormone binding / positive regulation of urine volume / regulation of osteoblast proliferation / G protein-coupled peptide receptor activity / negative regulation of systemic arterial blood pressure / hormone receptor binding / negative regulation of cold-induced thermogenesis / chloride ion binding / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / blood vessel remodeling / blood vessel diameter maintenance / negative regulation of angiogenesis / positive regulation of nitric-oxide synthase activity / skeletal system development / response to ischemia / peptide binding / hormone activity / negative regulation of cell growth / regulation of blood pressure / vasodilation / protein folding / angiogenesis / cell surface receptor signaling pathway / 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: 2.9 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 | 1yk1.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yk1.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yk1_validation.pdf.gz | 771.8 KB | Display | wwPDB validaton report |
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Full document | 1yk1_full_validation.pdf.gz | 801.9 KB | Display | |
Data in XML | 1yk1_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 1yk1_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/1yk1 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/1yk1 | HTTPS FTP |
-Related structure data
Related structure data | 1yk0C 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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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABE
#1: Protein | Mass: 52773.500 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: 2205.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P16860 |
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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, 323 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: 2.9→50 Å / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 |
Reflection shell | Resolution: 2.9→3.06 Å / Rmerge(I) obs: 0.492 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JDP Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.06 Å /
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