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Yorodumi- PDB-1t7h: X-ray structure of [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t7h | ||||||
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Title | X-ray structure of [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide | ||||||
Components | Endothelin-1Endothelin 1 | ||||||
Keywords | SIGNALING PROTEIN / endothelin / dimer / salt bridge / cysteine stabilized helical motif | ||||||
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 / endothelin B receptor binding / rhythmic excitation / 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 / endothelin B receptor binding / rhythmic excitation / peptide hormone secretion / neural crest cell fate commitment / sympathetic neuron axon guidance / body fluid secretion / glomerular endothelium development / vein smooth muscle contraction / noradrenergic neuron differentiation / response to prostaglandin F / positive regulation of renal sodium excretion / leukocyte activation / positive regulation of sarcomere organization / histamine secretion / rough endoplasmic reticulum lumen / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / 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 / podocyte differentiation / response to ozone / Weibel-Palade body / 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 / positive regulation of urine volume / regulation of pH / respiratory gaseous exchange by respiratory system / basal part of cell / positive regulation of smooth muscle contraction / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / protein kinase C-activating G protein-coupled receptor signaling pathway / embryonic heart tube development / negative regulation of blood coagulation / superoxide anion generation / dorsal/ventral pattern formation / axon extension / positive regulation of neutrophil chemotaxis / middle ear morphogenesis / positive regulation of signaling receptor activity / cellular response to glucocorticoid stimulus / cartilage development / 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 / response to dexamethasone / positive regulation of cardiac muscle hypertrophy / negative regulation of smooth muscle cell apoptotic process / membrane depolarization / thyroid gland development / positive regulation of cell size / regulation of vasoconstriction / canonical Wnt signaling pathway / cellular response to interleukin-1 / response to amino acid / 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 / mitochondrion organization / Peptide ligand-binding receptors / positive regulation of mitotic nuclear division / phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.13 Å | ||||||
Authors | Hoh, F. / Cerdan, R. / Kaas, Q. / Nishi, Y. / Chiche, L. / Kubo, S. / Chino, N. / Kobayashi, Y. / Dumas, C. / Aumelas, A. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: High-resolution X-ray structure of the unexpectedly stable dimer of the [Lys(-2)-Arg(-1)-des(17-21)]endothelin-1 peptide Authors: Hoh, F. / Cerdan, R. / Kaas, Q. / Nishi, Y. / Chiche, L. / Kubo, S. / Chino, N. / Kobayashi, Y. / Dumas, C. / Aumelas, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t7h.cif.gz | 23.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t7h.ent.gz | 18 KB | Display | PDB format |
PDBx/mmJSON format | 1t7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/1t7h ftp://data.pdbj.org/pub/pdb/validation_reports/t7/1t7h | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | the biological assembly is a dimer |
-Components
#1: Protein/peptide | Mass: 2143.554 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EDN1 / References: UniProt: P05305 #2: 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: 1.85 Å3/Da / Density % sol: 33 % |
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Crystal grow | Temperature: 291 K / pH: 5 Details: PEG 4000, isopropanol, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K, pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→18.3 Å / Num. obs: 12081 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07 |
Reflection shell | Resolution: 1.13→1.16 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.13→10 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.602 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 8.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.13→1.15 Å / Total num. of bins used: 20 /
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