[English] 日本語
Yorodumi
- SASDE39: Interleukin-18 receptor accessory protein ectodomain with Rα linker -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDE39
SampleInterleukin-18 receptor accessory protein ectodomain with Rα linker
  • Interleukin-18 receptor accessory protein ectodomain with Rα linker (protein), Homo sapiens
Function / homology
Function and homology information


interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / neutrophil activation / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / coreceptor activity ...interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / neutrophil activation / interleukin-18-mediated signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / coreceptor activity / cellular response to hydrogen peroxide / positive regulation of NF-kappaB transcription factor activity / cell population proliferation / inflammatory response / immune response / plasma membrane
Similarity search - Function
IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin ...IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-18 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: Structure / Year: 2019
Title: Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.
Authors: Jiwan Ge / Soumya G Remesh / Michal Hammel / Si Pan / Andrew D Mahan / Shuying Wang / Xinquan Wang /
Abstract: The interleukin 1 (IL-1) receptor family, whose members contain three immunoglobulin-like domains (D1-D3) in the extracellular region, is responsible for transmitting pleiotropic signals of IL-1 ...The interleukin 1 (IL-1) receptor family, whose members contain three immunoglobulin-like domains (D1-D3) in the extracellular region, is responsible for transmitting pleiotropic signals of IL-1 cytokines. The inter-domain flexibility of IL-1 receptors and its functional roles have not been fully elucidated. In this study, we used small-angle X-ray scattering to show that ligand-binding primary receptors and co-receptors in the family all have inherent inter-domain flexibility due to the D2/D3 linker. Variants of the IL-1RAcP and IL-18Rβ co-receptors with mutated D2/D3 linkers cannot form a cytokine-receptor complex and mediate signaling. Our analysis further revealed that these mutated co-receptors exhibited a changed conformational ensemble, suggesting that loss of function is due to the alteration of receptor dynamics. Taken together, our results demonstrate that the D2/D3 linker is a critical functional determinant of IL-1 receptor and underscore the important roles of the inter-domain flexibility in cytokine/receptor binding and signaling.
Contact author
  • Shu-Ying Wang (National Cheng Kung University, Taiwan)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2667
Type: atomic / Chi-square value: 1.04850536085
Search similar-shape structures of this assembly by Omokage search (details)
Model #2668
Type: atomic / Chi-square value: 1.04850536085
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Interleukin-18 receptor accessory protein ectodomain with Rα linker
Specimen concentration: 10 mg/ml
BufferName: 10mM HEPES, 150mM NaCl, 3% glycerol / pH: 7.2
Entity #1398Type: protein
Description: Interleukin-18 receptor accessory protein ectodomain with Rα linker
Formula weight: 41.405 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: O95256
Sequence: FNISGCSTKK LLWTYSTRSE EEFVLFCDLP EPQKSHFCHR NRLSPKQVPE HLPFMGSNDL SDVQWYQQPS NGDPLEDIRK SYPHIIQDKC TLHFLTPGVN NSGSYICRPK MIKSPYDVAC CVKMILEVKP QTNASCEYSA SHKQDLLLGS TGSISCPSLS CQSDAQSPAV ...Sequence:
FNISGCSTKK LLWTYSTRSE EEFVLFCDLP EPQKSHFCHR NRLSPKQVPE HLPFMGSNDL SDVQWYQQPS NGDPLEDIRK SYPHIIQDKC TLHFLTPGVN NSGSYICRPK MIKSPYDVAC CVKMILEVKP QTNASCEYSA SHKQDLLLGS TGSISCPSLS CQSDAQSPAV TWYKNGKLLS VERSNRIVVD EVYDYHQGTY VCDYTQSDTV SSWTVRAVVQ VRTVEDRSNI VPVILDPVED TLEVELGKPL TISCKARFGF ERVFNPVIKW YIKDSDLEWE VSVPEAKSIK STLKDEIIER NIILEKVTQR DLRRKFVCFV QNSIGNTTQS VQLKEKRAAA LHHILDAQKM VWNHRHHHHH H

-
Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 1.5 mm
DetectorName: Pilatus3 X 2M / Pixsize x: 172 mm
Scan
Title: Interleukin-18 receptor accessory protein ectodomain with Rα linker
Measurement date: Jul 24, 2017 / Cell temperature: 20 °C / Exposure time: 3 sec. / Number of frames: 600 / Unit: 1/A /
MinMax
Q0.012 0.5681
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 406 /
MinMax
Q0.01756 0.2433
P(R) point10 415
R0 115
Result
Type of curve: sec
Comments: SEC-SAXS was performed at 20°C using the following parameters: Column: Schodex kw-803 ; Flow rate: 0.5 mL/min; Total acquisition time: 30min; Sample injection concentration: 10 mg/mL; Injection volume: 50 μL.
ExperimentalPorod
MW53.7 kDa-
Volume-72 nm3

P(R)GuinierGuinier error
Forward scattering, I035.64 35.74 0.05
Radius of gyration, Rg3.34 nm3.38 nm0.01

MinMax
D-11.5
Guinier point1 51

+
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://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