[English] 日本語
Yorodumi
- PDB-5x93: Human endothelin receptor type-B in complex with antagonist K-8794 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5x93
TitleHuman endothelin receptor type-B in complex with antagonist K-8794
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 / 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
CHOLESTEROL / Chem-K87 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Endolysin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMar 5, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,55619
Polymers52,0841
Non-polymers5,47218
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-31 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.130, 147.480, 108.380
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-1218-

SO4

21A-1354-

HOH

31A-1404-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 52084.078 Da / Num. of mol.: 1
Mutation: R124Y,D154A,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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24530, UniProt: P00720, lysozyme

-
Non-polymers , 5 types, 124 molecules

#2: Chemical ChemComp-K87 / 3-[6-[(4-tert-butylphenyl)sulfonylamino]-5-(2-methoxyphenoxy)-2-pyrimidin-2-yl-pyrimidin-4-yl]oxy-N-(2,6-dimethylphenyl)propanamide


Mass: 682.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H38N6O6S
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 500 DME, (NH4)2SO4, MOPS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.941 Å / Num. obs: 40026 / % possible obs: 98.8 % / Redundancy: 6.98 % / Biso Wilson estimate: 38.29 Å2 / Net I/σ(I): 8.53

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→41.941 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1524 5 %
Rwork0.2106 28974 -
obs0.212 30498 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.73 Å2 / Biso mean: 57.1766 Å2 / Biso min: 24.16 Å2
Refinement stepCycle: final / Resolution: 2.2→41.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 364 106 3842
Biso mean--69.83 54.31 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053807
X-RAY DIFFRACTIONf_angle_d0.7595109
X-RAY DIFFRACTIONf_chiral_restr0.04570
X-RAY DIFFRACTIONf_plane_restr0.01606
X-RAY DIFFRACTIONf_dihedral_angle_d14.1832371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.27110.38211370.356625952732100
2.2711-2.35220.35261380.309726062744100
2.3522-2.44640.31711350.273325802715100
2.4464-2.55770.3031370.257426132750100
2.5577-2.69250.27671360.232625992735100
2.6925-2.86120.24071390.206626402779100
2.8612-3.08210.23351380.216326142752100
3.0821-3.39210.22851380.202926362774100
3.3921-3.88260.19911400.189926562796100
3.8826-4.89050.20841400.174226682808100
4.8905-41.94870.22011460.19862767291399

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more