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- PDB-5glh: Human endothelin receptor type-B in complex with ET-1 -

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Basic information

Entry
Database: PDB / ID: 5glh
TitleHuman endothelin receptor type-B in complex with ET-1
Components
  • Endothelin Receptor Subtype-B
  • Peptide from Endothelin-1
KeywordsSIGNALING PROTEIN / alpha helical
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / endothelin receptor activity ...enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / endothelin receptor activity / peptide hormone secretion / endothelin B receptor binding / aldosterone metabolic process / 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 / cellular response to mineralocorticoid stimulus / histamine secretion / neural crest cell fate commitment / regulation of fever generation / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / positive regulation of penile erection / sympathetic neuron axon guidance / positive regulation of sarcomere organization / noradrenergic neuron differentiation / leukocyte activation / body fluid secretion / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / rough endoplasmic reticulum lumen / heparin proteoglycan metabolic process / positive regulation of renal sodium excretion / neuroblast migration / : / posterior midgut development / pharyngeal arch artery morphogenesis / regulation of D-glucose transmembrane transport / positive regulation of odontogenesis / endothelin receptor signaling pathway involved in heart process / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / Weibel-Palade body / endothelin receptor signaling pathway / response to ozone / podocyte differentiation / developmental pigmentation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / response to sodium phosphate / renal sodium excretion / enteric nervous system development / positive regulation of cation channel activity / axonogenesis involved in innervation / glomerular filtration / protein transmembrane transport / renin secretion into blood stream / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / renal albumin absorption / melanocyte differentiation / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / regulation of pH / positive regulation of smooth muscle contraction / basal part of cell / peripheral nervous system development / response to salt / positive regulation of hormone secretion / type 1 angiotensin receptor binding / cellular response to toxic substance / 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 / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / establishment of endothelial barrier / signal transduction involved in regulation of gene expression / positive regulation of neutrophil chemotaxis / neural crest cell migration / prostaglandin biosynthetic process / superoxide anion generation / cellular response to glucocorticoid stimulus / cartilage development / middle ear morphogenesis / negative regulation of protein metabolic process / cGMP-mediated signaling / cellular response to fatty acid / nitric oxide transport / response to pain / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Phage lysozyme ...Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / 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)
Similarity search - Domain/homology
Endothelin-1 / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsShihoya, W. / Nishizawa, T. / Okuta, A. / Tani, K. / Fujiyoshi, Y. / Dohmae, N. / Nureki, O. / Doi, T.
CitationJournal: Nature / Year: 2016
Title: Activation mechanism of endothelin ETB receptor by endothelin-1.
Authors: Shihoya, W. / Nishizawa, T. / Okuta, A. / Tani, K. / Dohmae, N. / Fujiyoshi, Y. / Nureki, O. / Doi, T.
History
DepositionJul 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references / Structure summary
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 Subtype-B
B: Peptide from Endothelin-1


Theoretical massNumber of molelcules
Total (without water)58,4552
Polymers58,4552
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.970, 172.970, 109.350
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 Subtype-B


Mass: 55956.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EDNRB / Plasmid: modified pFastBac / Cell line (production host): Sf9 / Production host: spodoptera frugiperda (fall armyworm) / References: UniProt: P24530*PLUS
#2: Protein/peptide Peptide from Endothelin-1 / Preproendothelin-1 / PPET1


Mass: 2497.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05305
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 400, MES, (NH4)2SO4, 1,4-butanediol

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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: Nov 11, 2013
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17421 / % possible obs: 99.9 % / Redundancy: 15.2 % / Biso Wilson estimate: 70.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1543 / Net I/av σ(I): 14.63 / Net I/σ(I): 15.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.496 / Mean I/σ(I) obs: 1.76 / CC1/2: 0.975 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata processing
RefinementResolution: 2.8→46.214 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 1741 10 %
Rwork0.2336 15662 -
obs0.2379 17403 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.43 Å2 / Biso mean: 84.5266 Å2 / Biso min: 31.47 Å2
Refinement stepCycle: final / Resolution: 2.8→46.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 0 4 3643
Biso mean---76.23 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023720
X-RAY DIFFRACTIONf_angle_d0.4725072
X-RAY DIFFRACTIONf_chiral_restr0.036609
X-RAY DIFFRACTIONf_plane_restr0.004626
X-RAY DIFFRACTIONf_dihedral_angle_d15.1432209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.88250.34311420.319412741416100
2.8825-2.97550.37891420.328812761418100
2.9755-3.08180.36441410.292512821423100
3.0818-3.20520.32621450.279813031448100
3.2052-3.3510.29781450.258313001445100
3.351-3.52760.31441420.250612761418100
3.5276-3.74860.30631440.241513001444100
3.7486-4.03780.2871460.235113141460100
4.0378-4.44390.28771450.215312941439100
4.4439-5.08620.24321470.213913191466100
5.0862-6.40540.28921470.242613261473100
6.4054-46.22060.21111550.19531398155399

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