[English] 日本語
Yorodumi- PDB-6dk5: The X-ray crystal structure of human endothelin-1, a polypeptide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dk5 | ||||||
---|---|---|---|---|---|---|---|
Title | The X-ray crystal structure of human endothelin-1, a polypeptide hormone regulator of blood pressure | ||||||
Components | Endothelin-1 | ||||||
Keywords | HORMONE / blood pressure / vasoconstrictor / sarafotoxins / polypeptide / hypertension / diabetes / stroke | ||||||
Function / homology | Function and homology information positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment ...positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment / sympathetic neuron axon guidance / positive regulation of artery morphogenesis / glomerular endothelium development / vein smooth muscle contraction / body fluid secretion / noradrenergic neuron differentiation / response to prostaglandin F / positive regulation of sarcomere organization / leukocyte activation / positive regulation of renal sodium excretion / histamine secretion / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / regulation of glucose transmembrane transport / positive regulation of odontogenesis / endothelin receptor signaling pathway involved in heart process / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / endothelin receptor signaling pathway / Weibel-Palade body / podocyte differentiation / response to ozone / renal sodium ion absorption / glomerular filtration / positive regulation of cell growth involved in cardiac muscle cell development / artery smooth muscle contraction / axonogenesis involved in innervation / positive regulation of cation channel activity / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / basal part of cell / respiratory gaseous exchange by respiratory system / positive regulation of urine volume / positive regulation of smooth muscle contraction / response to salt / regulation of pH / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / : / embryonic heart tube development / negative regulation of blood coagulation / dorsal/ventral pattern formation / axon extension / superoxide anion generation / positive regulation of neutrophil chemotaxis / positive regulation of signaling receptor activity / cartilage development / middle ear morphogenesis / cellular response to glucocorticoid stimulus / prostaglandin biosynthetic process / negative regulation of protein metabolic process / nitric oxide transport / cellular response to fatty acid / branching involved in blood vessel morphogenesis / positive regulation of heart rate / : / response to testosterone / positive regulation of cardiac muscle hypertrophy / response to dexamethasone / negative regulation of smooth muscle cell apoptotic process / membrane depolarization / thyroid gland development / positive regulation of cell size / regulation of vasoconstriction / response to amino acid / canonical Wnt signaling pathway / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / positive regulation of JUN kinase activity / transport vesicle / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / protein kinase A signaling / response to amphetamine / cellular response to calcium ion / response to muscle stretch / ERK1 and ERK2 cascade / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of endothelial cell migration / positive regulation of mitotic nuclear division / mitochondrion organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | McPherson, A. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: The X-ray crystal structure of human endothelin 1, a polypeptide hormone regulator of blood pressure. Authors: McPherson, A. / Larson, S.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dk5.cif.gz | 21 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dk5.ent.gz | 12.6 KB | Display | PDB format |
PDBx/mmJSON format | 6dk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dk5_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6dk5_full_validation.pdf.gz | 433.5 KB | Display | |
Data in XML | 6dk5_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 6dk5_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dk5 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dk5 | HTTPS FTP |
-Related structure data
Related structure data | 5glhS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein/peptide | Mass: 2497.951 Da / Num. of mol.: 2 / Fragment: UNP residues 53-73 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05305 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.71 Å3/Da / Density % sol: 29.16 % Description: hexagonal prisms c. 400 um long, c. 150 um wide |
---|---|
Crystal grow | Temperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 4 uL 15 mg/mL aqueous endothelin + 6 uL reservoir solution (20-25% MPD, 0.2 M MES, pH 6.5) + 2 uL 0.2 M MES, pH 6.5 PH range: 6.0-7.0 / Temp details: 298-310 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1997 |
Radiation | Monochromator: Supper graphite crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→80 Å / Num. obs: 2534 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.947 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.086 / Rrim(I) all: 0.283 / Rsym value: 0.257 / Net I/av σ(I): 4.6 / Net I/σ(I): 4.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5GLH Resolution: 1.85→23.67 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.856 / SU B: 2.383 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.583 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.85→23.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|