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- PDB-6igk: Crystal Structure of human ETB receptor in complex with Endothelin-3 -

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Basic information

Entry
Database: PDB / ID: 6igk
TitleCrystal Structure of human ETB receptor in complex with Endothelin-3
Components
  • Endothelin receptor type B,Endolysin,Endothelin receptor type B
  • Endothelin-3
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / alpha helical / SIGNALING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / negative regulation of neuron maturation / chordate pharynx development / endothelin receptor activity / peptide hormone secretion / 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 / endothelin receptor activity / peptide hormone secretion / endothelin B receptor binding / aldosterone metabolic process / regulation of fever generation / vein smooth muscle contraction / intracellular magnesium ion homeostasis / positive regulation of penile erection / regulation of developmental pigmentation / heparin proteoglycan metabolic process / neuroblast migration / posterior midgut development / epithelial fluid transport / endothelin receptor signaling pathway / podocyte differentiation / developmental pigmentation / renal sodium ion absorption / response to sodium phosphate / renal sodium excretion / enteric nervous system development / protein transmembrane transport / renin secretion into blood stream / renal albumin absorption / melanocyte differentiation / regulation of pH / positive regulation of leukocyte chemotaxis / peripheral nervous system development / positive regulation of hormone secretion / type 1 angiotensin receptor binding / positive regulation of potassium ion transmembrane transport / negative regulation of adenylate cyclase activity / positive regulation of urine volume / regulation of systemic arterial blood pressure by endothelin / regulation of epithelial cell proliferation / vasoconstriction / axon extension / establishment of endothelial barrier / neural crest cell migration / blood circulation / negative regulation of protein metabolic process / cGMP-mediated signaling / response to pain / macrophage chemotaxis / peptide hormone binding / canonical Wnt signaling pathway / regulation of vasoconstriction / positive regulation of heart rate / viral release from host cell by cytolysis / potassium ion transmembrane transport / neutrophil chemotaxis / peptidoglycan catabolic process / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of MAP kinase activity / positive regulation of mitotic nuclear division / regulation of heart rate / axon guidance / Peptide ligand-binding receptors / establishment of localization in cell / positive regulation of cell differentiation / calcium-mediated signaling / : / hormone activity / calcium ion transmembrane transport / intracellular calcium ion homeostasis / cell wall macromolecule catabolic process / vasodilation / lysozyme / lysozyme activity / nervous system development / cell-cell signaling / regulation of gene expression / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / gene expression / nuclear membrane / G alpha (q) signalling events / positive regulation of canonical NF-kappaB signal transduction / host cell cytoplasm / cell population proliferation / cell surface receptor signaling pathway / defense response to bacterium / signaling receptor binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular region / 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 / G-protein coupled receptors family 1 signature. / Lysozyme-like domain superfamily / 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
CITRIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Endothelin-3 / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShihoya, W. / Izume, T. / Inoue, A. / Yamashita, K. / Kadji, F.M.N. / Hirata, K. / Aoki, J. / Nishizawa, T. / Nureki, O.
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
Revision 1.2Oct 23, 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
A: Endothelin receptor type B,Endolysin,Endothelin receptor type B
B: Endothelin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,07715
Polymers58,6072
Non-polymers4,47113
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.550, 172.280, 121.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 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 Endothelin-3 / ET-3 / Preproendothelin-3 / PPET3


Mass: 2650.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14138
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 500DME, Ammonium citrate tribasic

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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 27, 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→49.599 Å / Num. obs: 46829 / % possible obs: 100 % / Redundancy: 204.625 % / Biso Wilson estimate: 35.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.858 / Rrim(I) all: 0.86 / Χ2: 1.401 / Net I/σ(I): 20.7 / Num. measured all: 9582405 / Scaling rejects: 4327
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.12199.22818.0110.9574300.55918.057100
2.12-2.27207.8717.3922.0871870.8267.41100
2.27-2.45202.3323.7664.0264860.9393.775100
2.45-2.68209.2532.1127.459670.9762.117100
2.68-3211.961.13214.0655910.991.135100
3-3.46202.8270.58426.3348610.9960.585100
3.46-4.24194.8160.2595441620.9990.26100
4.24-5.99206.9540.1680.81326610.16100
5.99-49.599207.2830.1196.9118790.9970.1199.3

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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→49.599 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1998 4.27 %Random selection
Rwork0.1834 ---
obs0.1853 46782 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.61 Å2 / Biso mean: 47.0245 Å2 / Biso min: 20.75 Å2
Refinement stepCycle: final / Resolution: 2→49.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 296 175 4382
Biso mean--79.23 49.7 -
Num. residues----492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0001-2.05010.37021400.358331653305
2.0501-2.10550.28851400.27731473287
2.1055-2.16750.28741410.245631523293
2.1675-2.23750.27451420.207431743316
2.2375-2.31740.22531410.199331643305
2.3174-2.41020.24281410.183431693310
2.4102-2.51990.2181430.179831863329
2.5199-2.65270.22341420.166731713313
2.6527-2.81890.22081420.164932013343
2.8189-3.03660.18011420.166131833325
3.0366-3.34210.20231440.176832043348
3.3421-3.82550.24671440.162432423386
3.8255-4.81910.20941460.169632513397
4.8191-49.61450.22751500.186533753525
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.043-0.58770.39233.66910.26682.0854-0.1555-0.19410.20990.46770.1318-0.3781-0.3085-0.04260.01490.2994-0.0033-0.02040.31970.00320.21521.96742.034137.416
20.3646-0.88030.37144.3559-1.5421.1495-0.0249-0.1846-0.17580.29880.15770.4153-0.0102-0.0986-0.14650.17480.00210.03030.31180.04030.29368.12744.532129.735
33.0008-0.6271-1.31942.04540.36182.53330.01790.26940.068-0.5946-0.0291-0.3174-0.26730.19230.0190.4148-0.04880.0670.27060.00460.258911.81580.865103.41
40.7313-1.04160.27063.0778-1.46171.4084-0.0787-0.01680.16730.0028-0.0045-0.4246-0.18160.0360.06020.1718-0.00350.00290.26230.02290.263321.17744.992126.92
59.04352.89092.74453.8524.75325.9642-0.2036-0.3711-0.16240.3021-0.34151.2130.0029-1.07080.46890.3234-0.00750.01080.5014-0.0060.586711.10117.119129.353
62.12370.13160.39867.49190.21532.56040.0257-0.218-0.42630.109-0.0203-0.11410.2128-0.0515-0.01410.26150.03250.04490.32050.05290.298918.69922.59132.731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 86:164 )A86 - 164
2X-RAY DIFFRACTION2( CHAIN A AND RESID 165:303 ) or ( CHAIN A AND RESID 1000:1009 )A165 - 1009
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1010:1159 ) or ( CHAIN A AND RESID 311:312 )A312 - 1010
4X-RAY DIFFRACTION4( CHAIN A AND RESID 313:403 )A313 - 403
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:8 )B1 - 8
6X-RAY DIFFRACTION6( CHAIN B AND RESID 9:21 )B9 - 21

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