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- PDB-5xpr: Human endothelin receptor type-B in complex with antagonist bosentan -

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Entry
Database: PDB / ID: 5xpr
TitleHuman endothelin receptor type-B in complex with antagonist bosentan
ComponentsEndothelin B receptor,Endolysin,Endothelin B receptor
KeywordsSIGNALING PROTEIN / alpha helical
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / chordate pharynx development / vein smooth muscle contraction / regulation of fever generation / heparin metabolic process / positive regulation of penile erection ...enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / chordate pharynx development / vein smooth muscle contraction / regulation of fever generation / heparin metabolic process / positive regulation of penile erection / neuroblast migration / posterior midgut development / protein transmembrane transport / epithelial fluid transport / endothelin receptor signaling pathway / podocyte differentiation / developmental pigmentation / renal sodium ion absorption / response to sodium phosphate / enteric nervous system development / renal sodium excretion / renin secretion into blood stream / renal albumin absorption / melanocyte differentiation / positive regulation of urine volume / regulation of pH / negative regulation of adenylate cyclase activity / peripheral nervous system development / vasoconstriction / regulation of epithelial cell proliferation / type 1 angiotensin receptor binding / establishment of endothelial barrier / neural crest cell migration / negative regulation of protein metabolic process / response to pain / macrophage chemotaxis / cGMP-mediated signaling / peptide hormone binding / canonical Wnt signaling pathway / viral release from host cell by cytolysis / regulation of heart rate / Peptide ligand-binding receptors / peptidoglycan catabolic process / calcium-mediated signaling / calcium ion transmembrane transport / response to organic cyclic compound / vasodilation / cell wall macromolecule catabolic process / lysozyme / phospholipase C-activating G protein-coupled receptor signaling pathway / lysozyme activity / nervous system development / gene expression / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / host cell cytoplasm / cell surface receptor signaling pathway / defense response to bacterium / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like ...Endothelin receptor B / Endothelin receptor family / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Serpentine type 7TM GPCR chemoreceptor Srsx / 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) / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-K86 / Endolysin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsShihoya, W. / Nishizawa, T. / Yamashita, K. / Hirata, K. / Okuta, A. / Tani, K. / Fujiyoshi, Y. / Doi, T. / Nureki, O.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: X-ray structures of endothelin ETB receptor bound to clinical antagonist bosentan and its analog
Authors: Shihoya, W. / Nishizawa, T. / Yamashita, K. / Inoue, A. / Hirata, K. / Kadji, F.M.N. / Okuta, A. / Tani, K. / Aoki, J. / Fujiyoshi, Y. / Doi, T. / Nureki, O.
History
DepositionJun 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 15, 2017Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothelin B receptor,Endolysin,Endothelin B receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0646
Polymers52,1281
Non-polymers9365
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.720, 74.720, 218.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 52128.090 Da / Num. of mol.: 1
Mutation: R124Y,K270A,C1054A,I1094R,S342A,I381A,C396A,C400A,C405A
Source method: isolated from a genetically manipulated source
Details: Chimera protein of Residues 66-303 from P24530, linker, Residues 61-161 from P00720, Residues 311-407 from P24530.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: EDNRB, ETRB / Plasmid: modified pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P24530, UniProt: P00720, lysozyme
#2: Chemical ChemComp-K86 / 4-tert-butyl-N-[6-(2-hydroxyethyloxy)-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]benzenesulfonamide / Bosentan


Mass: 551.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29N5O6S / Comment: medication, antagonist*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 500 DME, Na2SO4, MOPS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→29.577 Å / Num. obs: 8691 / % possible obs: 98.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 93.57 Å2 / Net I/σ(I): 8.49

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→29.577 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2966 862 9.96 %
Rwork0.2476 7794 -
obs0.2525 8656 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.21 Å2 / Biso mean: 83.1479 Å2 / Biso min: 36.3 Å2
Refinement stepCycle: final / Resolution: 3.6→29.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 59 0 3229
Biso mean--78.98 --
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033301
X-RAY DIFFRACTIONf_angle_d0.6324509
X-RAY DIFFRACTIONf_chiral_restr0.039531
X-RAY DIFFRACTIONf_plane_restr0.005548
X-RAY DIFFRACTIONf_dihedral_angle_d18.1031926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.6001-3.82520.40411360.310312351371
3.8252-4.11980.2861430.279812831426
4.1198-4.53310.3271390.248912691408
4.5331-5.1860.28311380.239713061444
5.186-6.52220.34151460.279413091455
6.5222-29.57770.24661600.207413921552

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