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- PDB-1v6r: Solution Structure of Endothelin-1 with its C-terminal Folding -

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Basic information

Entry
Database: PDB / ID: 1v6r
TitleSolution Structure of Endothelin-1 with its C-terminal Folding
ComponentsEndothelin-1
KeywordsCONTRACTILE PROTEIN / endothelin / a-helix / c-terminal folding / cardiovascular bioactive peptide / g-protein coupled-receptor ligand
Function / homology
Function and homology information


: / endothelin A receptor binding / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of artery morphogenesis ...: / endothelin A receptor binding / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / peptide hormone secretion / endothelin B receptor binding / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of artery morphogenesis / cellular response to mineralocorticoid stimulus / histamine secretion / neural crest cell fate commitment / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / sympathetic neuron axon guidance / positive regulation of sarcomere organization / noradrenergic neuron differentiation / leukocyte activation / phospholipase D-activating G protein-coupled receptor signaling pathway / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / body fluid secretion / rough endoplasmic reticulum lumen / positive regulation of renal sodium excretion / pharyngeal arch artery morphogenesis / regulation of D-glucose transmembrane transport / endothelin receptor signaling pathway involved in heart process / positive regulation of odontogenesis / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to ozone / Weibel-Palade body / endothelin receptor signaling pathway / podocyte differentiation / positive regulation of cation channel activity / positive regulation of cell growth involved in cardiac muscle cell development / response to leptin / renal sodium ion absorption / axonogenesis involved in innervation / glomerular filtration / positive regulation of smooth muscle contraction / artery smooth muscle contraction / positive regulation of prostaglandin secretion / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / vasoconstriction / respiratory gaseous exchange by respiratory system / regulation of pH / basal part of cell / positive regulation of hormone secretion / response to salt / positive regulation of urine volume / regulation of systemic arterial blood pressure by endothelin / cellular response to toxic substance / embryonic heart tube development / dorsal/ventral pattern formation / cellular response to fatty acid / axon extension / cartilage development / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / superoxide anion generation / signal transduction involved in regulation of gene expression / negative regulation of protein metabolic process / middle ear morphogenesis / nitric oxide transport / cellular response to glucocorticoid stimulus / branching involved in blood vessel morphogenesis / response to dexamethasone / positive regulation of cardiac muscle hypertrophy / response to testosterone / negative regulation of smooth muscle cell apoptotic process / thyroid gland development / cAMP/PKA signal transduction / membrane depolarization / cellular response to interleukin-1 / negative regulation of blood coagulation / positive regulation of cell size / canonical Wnt signaling pathway / response to amino acid / regulation of vasoconstriction / cellular response to transforming growth factor beta stimulus / positive regulation of heart rate / transport vesicle / positive regulation of vascular associated smooth muscle cell proliferation / response to muscle stretch / ERK1 and ERK2 cascade / Transcriptional and post-translational regulation of MITF-M expression and activity / response to amphetamine / positive regulation of endothelial cell migration / positive regulation of mitotic nuclear division / positive regulation of calcium-mediated signaling / cellular response to calcium ion / Peptide ligand-binding receptors / response to activity / cytokine activity / response to nicotine
Similarity search - Function
Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / Endothelin family / Endothelin family signature. / Endothelin
Similarity search - Domain/homology
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsTakashima, H. / Mimura, N. / Ohkubo, T. / Yoshida, T. / Tamaoki, H. / Kobayashi, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination: Applied for Bioactive Peptide Endothelin-1 To Determine C-Terminal Folding
Authors: Takashima, H. / Mimura, N. / Ohkubo, T. / Yoshida, T. / Tamaoki, H. / Kobayashi, Y.
History
DepositionDec 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)2,4981
Polymers2,4981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 32000structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Endothelin-1 / ET-1


Mass: 2497.951 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in humans.
References: UniProt: P05305
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1312D TOCSY

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Sample preparation

DetailsContents: 2.5mM Endothelin-1 / Solvent system: 90% H2O, 5% D2O, 5% deuterated acetic acid
Sample conditionsIonic strength: 5% acetic acid / pH: 3 / Pressure: ambient / Temperature: 297.7 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.0.6Schwieters, C.D.structure solution
XPLOR-NIH2.0.6Schwieters, C.D.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: Distributed Computing based structure calculation to explore the conformational space comprehensively.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 32000 / Conformers submitted total number: 20

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