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- PDB-6dk5: The X-ray crystal structure of human endothelin-1, a polypeptide ... -

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Basic information

Entry
Database: PDB / ID: 6dk5
TitleThe X-ray crystal structure of human endothelin-1, a polypeptide hormone regulator of blood pressure
ComponentsEndothelin-1
KeywordsHORMONE / blood pressure / vasoconstrictor / sarafotoxins / polypeptide / hypertension / diabetes / stroke
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 / neural crest cell fate commitment ...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 / neural crest cell fate commitment / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / sympathetic neuron axon guidance / noradrenergic neuron differentiation / histamine secretion / positive regulation of chemokine-mediated signaling pathway / leukocyte activation / maternal process involved in parturition / rough endoplasmic reticulum lumen / phospholipase D-activating G protein-coupled receptor signaling pathway / body fluid secretion / positive regulation of sarcomere organization / 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 / positive regulation of cation channel activity / heparin proteoglycan metabolic process / Weibel-Palade body / podocyte differentiation / response to ozone / endothelin receptor signaling pathway / positive regulation of cell growth involved in cardiac muscle cell development / response to leptin / axonogenesis involved in innervation / glomerular filtration / cellular response to follicle-stimulating hormone stimulus / renal sodium ion absorption / renal albumin absorption / artery smooth muscle contraction / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / protein transmembrane transport / positive regulation of prostaglandin biosynthetic process / cellular response to mineralocorticoid stimulus / regulation of pH / positive regulation of smooth muscle contraction / respiratory gaseous exchange by respiratory system / positive regulation of renal sodium excretion / vasoconstriction / basal part of cell / response to salt / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / signal transduction involved in regulation of gene expression / axon extension / dorsal/ventral pattern formation / embryonic heart tube development / cellular response to toxic substance / cellular response to fatty acid / cartilage development / establishment of endothelial barrier / positive regulation of neutrophil chemotaxis / positive regulation of urine volume / negative regulation of protein metabolic process / superoxide anion generation / cellular response to glucocorticoid stimulus / nitric oxide transport / response to dexamethasone / branching involved in blood vessel morphogenesis / middle ear morphogenesis / response to testosterone / positive regulation of cardiac muscle hypertrophy / negative regulation of smooth muscle cell apoptotic process / thyroid gland development / negative regulation of blood coagulation / response to amino acid / positive regulation of cell size / membrane depolarization / cellular response to interleukin-1 / canonical Wnt signaling pathway / cAMP/PKA signal transduction / cellular response to transforming growth factor beta stimulus / regulation of vasoconstriction / positive regulation of heart rate / transport vesicle / positive regulation of vascular associated smooth muscle cell proliferation / ERK1 and ERK2 cascade / response to muscle stretch / positive regulation of mitotic nuclear division / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of endothelial cell migration / positive regulation of calcium-mediated signaling / positive regulation of smooth muscle cell proliferation / cellular response to calcium ion / cytokine 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMcPherson, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2019
Title: The X-ray crystal structure of human endothelin 1, a polypeptide hormone regulator of blood pressure.
Authors: McPherson, A. / Larson, S.B.
History
DepositionMay 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Endothelin-1
A: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)4,9962
Polymers4,9962
Non-polymers00
Water43224
1
A: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)2,4981
Polymers2,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endothelin-1


Theoretical massNumber of molelcules
Total (without water)2,4981
Polymers2,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.328, 27.328, 79.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein/peptide Endothelin-1 / Preproendothelin-1 / PPET1


Mass: 2497.951 Da / Num. of mol.: 2 / Fragment: UNP residues 53-73 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05305
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.71 Å3/Da / Density % sol: 29.16 %
Description: hexagonal prisms c. 400 um long, c. 150 um wide
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4 uL 15 mg/mL aqueous endothelin + 6 uL reservoir solution (20-25% MPD, 0.2 M MES, pH 6.5) + 2 uL 0.2 M MES, pH 6.5
PH range: 6.0-7.0 / Temp details: 298-310

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 15, 1997
RadiationMonochromator: Supper graphite crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→80 Å / Num. obs: 2534 / % possible obs: 99.6 % / Redundancy: 7.7 % / CC1/2: 0.947 / Rmerge(I) obs: 0.257 / Rpim(I) all: 0.086 / Rrim(I) all: 0.283 / Rsym value: 0.257 / Net I/av σ(I): 4.6 / Net I/σ(I): 4.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SDMSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GLH

5glh


Resolution: 1.85→23.67 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.856 / SU B: 2.383 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28373 143 5.3 %RANDOM
Rwork0.20387 ---
obs0.2079 2534 92.92 %-
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: 32.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.85→23.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms334 0 0 24 358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019346
X-RAY DIFFRACTIONr_bond_other_d0.0010.02306
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.92468
X-RAY DIFFRACTIONr_angle_other_deg0.8833712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.03540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.17623.33312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.161560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0960.252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0274
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1713.375166
X-RAY DIFFRACTIONr_mcbond_other3.1443.365165
X-RAY DIFFRACTIONr_mcangle_it4.6355.046204
X-RAY DIFFRACTIONr_mcangle_other4.6295.054205
X-RAY DIFFRACTIONr_scbond_it2.6963.426180
X-RAY DIFFRACTIONr_scbond_other2.693.424181
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9945.166265
X-RAY DIFFRACTIONr_long_range_B_refined7.75962.3131193
X-RAY DIFFRACTIONr_long_range_B_other7.75262.4031186
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.061 17 -
Rwork0.046 178 -
obs--88.64 %

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