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- PDB-1t7h: X-ray structure of [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide -

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Basic information

Entry
Database: PDB / ID: 1t7h
TitleX-ray structure of [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1 peptide
ComponentsEndothelin-1
KeywordsSIGNALING PROTEIN / endothelin / dimer / salt bridge / cysteine stabilized helical motif
Function / homology
Function and homology information


: / endothelin A receptor binding / phospholipase D-activating G protein-coupled receptor signaling pathway / 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 ...: / endothelin A receptor binding / phospholipase D-activating G protein-coupled receptor signaling pathway / 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 / body fluid secretion / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / rough endoplasmic reticulum lumen / positive regulation of renal sodium excretion / : / pharyngeal arch artery morphogenesis / regulation of D-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 / Weibel-Palade body / endothelin receptor signaling pathway / response to ozone / podocyte differentiation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / positive regulation of cation channel activity / axonogenesis involved in innervation / glomerular filtration / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / regulation of pH / positive regulation of smooth muscle contraction / basal part of cell / response to salt / positive regulation of hormone secretion / cellular response to toxic substance / positive regulation of urine volume / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / signal transduction involved in regulation of gene expression / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / superoxide anion generation / cellular response to glucocorticoid stimulus / cartilage development / middle ear morphogenesis / negative regulation of protein metabolic process / cellular response to fatty acid / nitric oxide transport / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy / negative regulation of smooth muscle cell apoptotic process / response to testosterone / response to dexamethasone / thyroid gland development / cAMP/PKA signal transduction / cellular response to interleukin-1 / membrane depolarization / negative regulation of blood coagulation / positive regulation of cell size / response to amino acid / canonical Wnt signaling pathway / regulation of vasoconstriction / positive regulation of heart rate / transport vesicle / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / response to muscle stretch / positive regulation of endothelial cell migration / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / response to amphetamine / positive regulation of mitotic nuclear division / positive regulation of calcium-mediated signaling / cellular response to calcium ion / positive regulation of DNA-binding transcription factor activity / Peptide ligand-binding receptors
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 / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.13 Å
AuthorsHoh, F. / Cerdan, R. / Kaas, Q. / Nishi, Y. / Chiche, L. / Kubo, S. / Chino, N. / Kobayashi, Y. / Dumas, C. / Aumelas, A.
CitationJournal: 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
DepositionMay 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 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
B: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)4,2872
Polymers4,2872
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-3 kcal/mol
Surface area2810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.136, 53.926, 19.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-36-

HOH

21B-31-

HOH

Detailsthe biological assembly is a dimer

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Components

#1: Protein/peptide Endothelin-1 / ET-1 / [Lys(-2)-Arg(-1)-des(17-21)]-endothelin-1


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 / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 291 K / pH: 5
Details: PEG 4000, isopropanol, sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K, pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.13→18.3 Å / Num. obs: 12081 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.07
Reflection shellResolution: 1.13→1.16 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
CCP4(SCALA)data scaling
SnBphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.134 613 4.8 %RANDOM
Rwork0.12 ---
obs0.122 12054 99.2 %-
all-12054 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.13→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms307 0 0 58 365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021315
X-RAY DIFFRACTIONr_bond_other_d0.0030.02272
X-RAY DIFFRACTIONr_angle_refined_deg1.931.986417
X-RAY DIFFRACTIONr_angle_other_deg1.0363647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.344534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.31322.30813
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9891570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.892152
X-RAY DIFFRACTIONr_chiral_restr0.1340.245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02318
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0264
X-RAY DIFFRACTIONr_nbd_refined0.2160.291
X-RAY DIFFRACTIONr_nbd_other0.260.2325
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.1841.5238
X-RAY DIFFRACTIONr_mcbond_other0.651.576
X-RAY DIFFRACTIONr_mcangle_it2.4622301
X-RAY DIFFRACTIONr_scbond_it3.7223155
X-RAY DIFFRACTIONr_scangle_it4.6194.5116
X-RAY DIFFRACTIONr_rigid_bond_restr1.8533709
X-RAY DIFFRACTIONr_sphericity_free8.41358
X-RAY DIFFRACTIONr_sphericity_bonded3.3313579
LS refinement shellResolution: 1.13→1.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.17 49
Rwork0.151 803

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