[English] 日本語
Yorodumi
- PDB-1v6r: Solution Structure of Endothelin-1 with its C-terminal Folding -

+
Open data


ID or keywords:

Loading...

-
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


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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more