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- PDB-1edn: HUMAN ENDOTHELIN-1 -

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Basic information

Entry
Database: PDB / ID: 1edn
TitleHUMAN ENDOTHELIN-1
ComponentsENDOTHELIN-1
KeywordsVASOCONSTRICTOR / SIGNAL POLYPEPTIDE 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 / 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 / phospholipase D-activating G protein-coupled receptor signaling pathway / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / leukocyte activation / rough endoplasmic reticulum lumen / body fluid secretion / 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 / glomerular filtration / axonogenesis involved in innervation / renal sodium ion absorption / positive regulation of smooth muscle contraction / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / cellular response to luteinizing hormone stimulus / regulation of pH / cellular response to mineralocorticoid stimulus / basal part of cell / vasoconstriction / response to salt / positive regulation of urine volume / positive regulation of hormone secretion / 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 / signal transduction involved in regulation of gene expression / superoxide anion generation / negative regulation of protein metabolic process / middle ear morphogenesis / cellular response to glucocorticoid stimulus / nitric oxide transport / 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 / negative regulation of blood coagulation / cellular response to interleukin-1 / membrane depolarization / 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 / positive regulation of smooth muscle cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / 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 amphetamine / cytokine activity / response to activity
Similarity search - Function
Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / Endothelin family / Endothelin family signature. / Endothelin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.18 Å
AuthorsWallace, B.A. / Janes, R.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: The crystal structure of human endothelin.
Authors: Janes, R.W. / Peapus, D.H. / Wallace, B.A.
#1: Journal: To be Published
Title: Comparison of the Structure of the Endothelin Receptor Agonist Bq123 with the Crystal Structure of the C-Terminal Tail of Endothelin
Authors: Peishoff, C.E. / Janes, R.W. / Wallace, B.A.
#2: Journal: Protein Sci. / Year: 1995
Title: A Comparison of X-Ray and NMR Structures for Human Endothelin-1
Authors: Wallace, B.A. / Janes, R.W. / Bassolino, D. / Krystek Junior, S.
History
DepositionSep 19, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
A: ENDOTHELIN-1

A: ENDOTHELIN-1


Theoretical massNumber of molelcules
Total (without water)4,9962
Polymers4,9962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Unit cell
Length a, b, c (Å)33.350, 33.350, 59.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide ENDOTHELIN-1


Mass: 2497.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P05305
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.43 %
Crystal grow
*PLUS
Method: x-ray capillaries
Components of the solutions
*PLUS
Conc.: 9 mg/ml

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 12, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.18→8 Å / Num. obs: 1876 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.107
Reflection
*PLUS
Num. measured all: 8907 / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.18→8 Å / σ(F): 3 /
RfactorNum. reflection% reflection
obs0.199 8907 75 %
Refinement stepCycle: LAST / Resolution: 2.18→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms171 0 0 0 171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3.96
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d26.8
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d2.8
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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