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- PDB-6igl: Crystal Structure of human ETB receptor in complex with IRL1620 -

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Basic information

Entry
Database: PDB / ID: 6igl
TitleCrystal Structure of human ETB receptor in complex with IRL1620
Components
  • Endothelin receptor type B,Endolysin,Endothelin receptor type B
  • IRL1620
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / alpha helical / SIGNALING PROTEIN / SIGNALING PROTEIN-PROTEIN BINDING complex
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 / epithelial fluid transport / endothelin receptor signaling pathway / developmental pigmentation / podocyte differentiation / renal sodium ion absorption / protein transmembrane transport / response to sodium phosphate / enteric nervous system development / renal sodium excretion / renin secretion into blood stream / melanocyte differentiation / renal albumin absorption / 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 / cGMP-mediated signaling / macrophage chemotaxis / peptide hormone binding / canonical Wnt signaling pathway / viral release from host cell by cytolysis / regulation of heart rate / peptidoglycan catabolic process / Peptide ligand-binding receptors / calcium-mediated signaling / calcium ion transmembrane transport / response to organic cyclic compound / vasodilation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / gene expression / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / cellular response to lipopolysaccharide / nuclear membrane / positive regulation of canonical NF-kappaB signal transduction / 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
CITRIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShihoya, W. / Izume, T. / Inoue, A. / Yamashita, K. / kadji, F.M.N. / Hirata, K. / Aoki, J. / Nishizawa, T. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Nat Commun / Year: 2018
Title: Crystal structures of human ETBreceptor provide mechanistic insight into receptor activation and partial activation.
Authors: Shihoya, W. / Izume, T. / Inoue, A. / Yamashita, K. / Kadji, F.M.N. / Hirata, K. / Aoki, J. / Nishizawa, T. / Nureki, O.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelin receptor type B,Endolysin,Endothelin receptor type B
B: IRL1620
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,42510
Polymers57,7792
Non-polymers1,6468
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-66 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.980, 303.860, 60.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1353-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 55956.727 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 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P24530, UniProt: A0A097J809, lysozyme
#2: Protein/peptide IRL1620


Mass: 1821.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 67 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 3.95 Å3/Da / Density % sol: 68.89 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG 500DME, (NH4)2SO4 or NH4Cl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 24, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47.162 Å / Num. obs: 25797 / % possible obs: 99.988372093 % / Observed criterion σ(I): -3 / Redundancy: 21.5064542389 % / CC1/2: 0.981196567801 / Rmerge(I) obs: 0.486369495494 / Net I/σ(I): 9.04695445316 / Num. measured all: 554802
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
2.7-2.7964998110621.52739456055.6819294967625370.3824577200351
2.79649981106-2.9084517556121.27312081862.9442355313125410.4942121134731
2.90845175561-3.0407986595220.82696097751.6838709248225370.6551469251751
3.04079865952-3.2010819886820.26795580111.4747599838625340.764729362711
3.20108198868-3.4015863295921.64118564741.0402224237825640.8129110327211
3.40158632959-3.6641332829122.41417322830.6481670674425400.9177170923851
3.66413328291-4.0326904840622.79238754330.40572802257626010.9630557938671
4.03269048406-4.6157975434322.28466305190.28287386649125820.9678380385541
4.61579754343-5.8137251069320.94859992330.23288769702626070.9777709524151
5.81372510693-47.169011400821.08932461870.12144489225927540.9943385455041

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GLH

5glh


Resolution: 2.7→47.162 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1288 5 %Random selection
Rwork0.2066 24476 --
obs0.2083 25764 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.24 Å2 / Biso mean: 63.1481 Å2 / Biso min: 5.18 Å2
Refinement stepCycle: final / Resolution: 2.7→47.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3863 0 108 59 4030
Biso mean--71.24 40 -
Num. residues----484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.80810.3421390.28326632802
2.8081-2.93590.29381410.243726662807
2.9359-3.09060.25381410.221426802821
3.0906-3.28420.25451410.22126902831
3.2842-3.53770.22991440.20627152859
3.5377-3.89360.23731410.190527102851
3.8936-4.45660.22281440.189527192863
4.4566-5.61340.2271440.190927512895
5.6134-47.1690.22451530.203728823035

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