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- PDB-6lry: Crystal structure of human endothelin ETB receptor in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6lry
TitleCrystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b
Components
  • Endothelin receptor type B,Endolysin,Endothelin receptor type B
  • Sarafotoxin-B
KeywordsMEMBRANE PROTEIN / alpha helical / SIGNALING PROTEIN
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / negative regulation of neuron maturation / chordate pharynx development / neuroblast migration / endothelin receptor activity / endothelin B receptor binding / aldosterone metabolic process / regulation of fever generation / vein smooth muscle contraction ...enteric smooth muscle cell differentiation / response to endothelin / negative regulation of neuron maturation / chordate pharynx development / neuroblast migration / endothelin receptor activity / endothelin B receptor binding / aldosterone metabolic process / regulation of fever generation / vein smooth muscle contraction / positive regulation of penile erection / heparin proteoglycan metabolic process / posterior midgut development / epithelial fluid transport / endothelin receptor signaling pathway / podocyte differentiation / developmental pigmentation / renal sodium excretion / response to sodium phosphate / enteric nervous system development / protein transmembrane transport / renal sodium ion absorption / renin secretion into blood stream / renal albumin absorption / regulation of pH / melanocyte differentiation / vasoconstriction / peripheral nervous system development / type 1 angiotensin receptor binding / negative regulation of adenylate cyclase activity / positive regulation of urine volume / regulation of epithelial cell proliferation / regulation of systemic arterial blood pressure by endothelin / establishment of endothelial barrier / neural crest cell migration / negative regulation of protein metabolic process / : / response to pain / macrophage chemotaxis / peptide hormone binding / canonical Wnt signaling pathway / regulation of vasoconstriction / viral release from host cell by cytolysis / peptidoglycan catabolic process / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of heart rate / Peptide ligand-binding receptors / calcium-mediated signaling / hormone activity / calcium ion transmembrane transport / vasodilation / intracellular calcium ion homeostasis / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / nervous system development / cellular response to lipopolysaccharide / toxin activity / positive regulation of cytosolic calcium ion concentration / nuclear membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / G alpha (q) signalling events / host cell cytoplasm / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular space / plasma membrane
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Endolysin T4 type ...Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / Lysozyme-like domain superfamily / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Endolysin / Sarafotoxin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
Atractaspis engaddensis (Israeli mole viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsIzume, T. / Miyauchi, H. / Shihoya, W. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06294 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of human endothelin ETBreceptor in complex with sarafotoxin S6b.
Authors: Izume, T. / Miyauchi, H. / Shihoya, W. / Nureki, O.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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 1.3Oct 16, 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 receptor type B,Endolysin,Endothelin receptor type B
B: Sarafotoxin-B


Theoretical massNumber of molelcules
Total (without water)59,3232
Polymers59,3232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-19 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.120, 82.280, 166.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Endothelin receptor type B,Endolysin,Endothelin receptor type B / ET-BR / Endothelin receptor non-selective type / Lysis protein / Lysozyme / Muramidase


Mass: 56751.574 Da / Num. of mol.: 1
Mutation: R124Y,D154A,K270A,C1052T,C1095A,S342A,I381A,C396A,C400A,C405A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of Endothelin receptor type B inserted with Endolysin between residues 303 and 311.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage RB59 (virus)
Gene: EDNRB, ETRB, e, RB59_126 / Plasmid: modified pFastBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24530, UniProt: A0A097J809, lysozyme
#2: Protein/peptide Sarafotoxin-B / sarafotoxin S6b


Mass: 2570.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Atractaspis engaddensis (Israeli mole viper)
References: UniProt: P13208
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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG 600, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.3 Å / Num. obs: 17494 / % possible obs: 99.75 % / Redundancy: 19.3 % / CC1/2: 0.994 / Net I/σ(I): 9.06
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1724 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IGK

6igk


Resolution: 3→49.297 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3037 845 4.84 %
Rwork0.2698 16623 -
obs0.2714 17468 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.94 Å2 / Biso mean: 100.0878 Å2 / Biso min: 49.78 Å2
Refinement stepCycle: final / Resolution: 3→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 0 0 3881
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0001-3.1880.421320.39252727
3.188-3.43410.37571310.33712739
3.4341-3.77960.33881340.28232735
3.7796-4.32620.26281450.25482738
4.3262-5.44950.30541430.25272779
5.4495-49.2970.27741600.24712905

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