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- PDB-5gli: Human endothelin receptor type-B in the ligand-free form -

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Basic information

Entry
Database: PDB / ID: 5gli
TitleHuman endothelin receptor type-B in the ligand-free form
ComponentsEndothelin Receptor Subtype-B
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 / 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 / regulation of heart rate / Peptide ligand-binding receptors / calcium-mediated signaling / calcium ion transmembrane transport / response to organic cyclic compound / vasodilation / 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 / cell surface receptor signaling pathway / 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 / 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
OLEIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endothelin Receptor Subtype-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5609
Polymers52,0841
Non-polymers1,4768
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.980, 147.540, 107.810
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: 52084.078 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: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.3 / Details: MES, PEG 350 MME, (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: Jul 22, 2015
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20780 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 43.09 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.2383 / Net I/av σ(I): 8.29 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8 % / Rmerge(I) obs: 1.933 / Mean I/σ(I) obs: 1.1 / CC1/2: 0.535 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata processing
RefinementResolution: 2.5→43.523 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 2077 10 %
Rwork0.247 18686 -
obs0.25 20763 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123 Å2 / Biso mean: 50.4695 Å2 / Biso min: 22.09 Å2
Refinement stepCycle: final / Resolution: 2.5→43.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 82 24 3451
Biso mean--60.6 39.98 -
Num. residues----429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023499
X-RAY DIFFRACTIONf_angle_d0.4364750
X-RAY DIFFRACTIONf_chiral_restr0.035551
X-RAY DIFFRACTIONf_plane_restr0.005579
X-RAY DIFFRACTIONf_dihedral_angle_d15.92075
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.55820.35611350.3612241359100
2.5582-2.62210.39821360.342412141350100
2.6221-2.6930.36641340.33312181352100
2.693-2.77230.35581390.289612501389100
2.7723-2.86170.32871370.266512221359100
2.8617-2.9640.36441380.290712461384100
2.964-3.08260.33171360.29812261362100
3.0826-3.22290.28781370.257412271364100
3.2229-3.39270.31791370.251612431380100
3.3927-3.60520.23921380.222212391377100
3.6052-3.88340.26461400.222412561396100
3.8834-4.27390.23561390.20112461385100
4.2739-4.89160.23671400.201712681408100
4.8916-6.16020.24691430.251412771420100
6.1602-43.53010.23841480.24251330147899

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