[English] 日本語
Yorodumi
- PDB-6lry: Crystal structure of human endothelin ETB receptor in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lry
TitleCrystal structure of human endothelin ETB receptor in complex with sarafotoxin S6b
Components
  • Endothelin receptor type B,Endolysin,Endothelin receptor type B
  • Sarafotoxin-B
KeywordsMEMBRANE PROTEIN / alpha helical / SIGNALING PROTEIN
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 / endothelin B receptor binding / vein smooth muscle contraction / regulation of fever generation / heparin metabolic process ...enteric smooth muscle cell differentiation / response to endothelin / endothelin receptor activity / negative regulation of neuron maturation / aldosterone metabolic process / chordate pharynx development / endothelin B receptor binding / 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 / regulation of systemic arterial blood pressure by endothelin / 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 / regulation of vasoconstriction / 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 / hormone activity / intracellular calcium ion homeostasis / vasodilation / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / phospholipase C-activating G protein-coupled receptor signaling pathway / nervous system development / gene expression / toxin activity / 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 / extracellular space / 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 / T4-type lysozyme ...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 / 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
Endolysin / Sarafotoxin / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage RB59 (virus)
Atractaspis engaddensis (Israeli mole viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsIzume, T. / Miyauchi, H. / Shihoya, W. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06294 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of human endothelin ETBreceptor in complex with sarafotoxin S6b.
Authors: Izume, T. / Miyauchi, H. / Shihoya, W. / Nureki, O.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endothelin receptor type B,Endolysin,Endothelin receptor type B
B: Sarafotoxin-B


Theoretical massNumber of molelcules
Total (without water)59,3232
Polymers59,3232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-19 kcal/mol
Surface area24750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.120, 82.280, 166.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

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


Mass: 56751.574 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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24530, UniProt: A0A097J809, lysozyme
#2: Protein/peptide Sarafotoxin-B / sarafotoxin S6b


Mass: 2570.980 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Atractaspis engaddensis (Israeli mole viper)
References: UniProt: P13208

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: PEG 600, Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 10, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.3 Å / Num. obs: 17494 / % possible obs: 99.75 % / Redundancy: 19.3 % / CC1/2: 0.994 / Net I/σ(I): 9.06
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1724 / CC1/2: 0.545

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IGK

6igk


Resolution: 3→49.297 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3037 845 4.84 %
Rwork0.2698 16623 -
obs0.2714 17468 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.94 Å2 / Biso mean: 100.0878 Å2 / Biso min: 49.78 Å2
Refinement stepCycle: final / Resolution: 3→49.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 0 0 3881
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0001-3.1880.421320.39252727
3.188-3.43410.37571310.33712739
3.4341-3.77960.33881340.28232735
3.7796-4.32620.26281450.25482738
4.3262-5.44950.30541430.25272779
5.4495-49.2970.27741600.24712905

+
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