[English] 日本語
Yorodumi
- PDB-7fch: IL-18Rbeta TIR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fch
TitleIL-18Rbeta TIR domain
ComponentsInterleukin-18 receptor accessory protein
KeywordsIMMUNE SYSTEM / IL-18Rbeta / TIR domain / receptor protein
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 / interleukin-18-mediated signaling pathway / neutrophil activation / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / coreceptor activity / positive regulation of NF-kappaB transcription factor activity ...interleukin-18 receptor activity / interleukin-18 receptor complex / Interleukin-18 signaling / positive regulation of natural killer cell mediated cytotoxicity / interleukin-18-mediated signaling pathway / neutrophil activation / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / coreceptor activity / positive regulation of NF-kappaB transcription factor activity / cellular response to hydrogen peroxide / adaptive immune response / cell population proliferation / immune response / inflammatory response / cell surface / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.883 Å
AuthorsWang, X. / Zhou, J.
CitationJournal: Iscience / Year: 2022
Title: Structural basis of the IL-1 receptor TIR domain-mediated IL-1 signaling
Authors: Zhou, J. / Xiao, Y. / Ren, Y. / Ge, J. / Wang, X.
History
DepositionJul 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interleukin-18 receptor accessory protein
B: Interleukin-18 receptor accessory protein
C: Interleukin-18 receptor accessory protein
D: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)76,3124
Polymers76,3124
Non-polymers00
Water3,135174
1
A: Interleukin-18 receptor accessory protein

C: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)38,1562
Polymers38,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area1330 Å2
ΔGint-12 kcal/mol
Surface area13990 Å2
MethodPISA
2
B: Interleukin-18 receptor accessory protein
D: Interleukin-18 receptor accessory protein


Theoretical massNumber of molelcules
Total (without water)38,1562
Polymers38,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-14 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.760, 161.074, 52.164
Angle α, β, γ (deg.)90.000, 112.440, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Interleukin-18 receptor accessory protein / IL-18 receptor accessory protein / IL-18RAcP


Mass: 19078.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18RAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O95256, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium tartrate dibasic, pH 6.25, 20% w/v PEG3350, 3% v/v (+/-)-2-Methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.48
ReflectionResolution: 1.88→50 Å / Num. obs: 46801 / % possible obs: 95.61 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 4060

-
Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FCC

7fcc


Resolution: 1.883→48.214 Å / Cross valid method: THROUGHOUT / σ(F): 9.37 / Phase error: 28.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2226 2316 4.96 %
Rwork0.1864 44424 -
obs0.2 46711 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 35.5059 Å2 / Biso min: 17.23 Å2
Refinement stepCycle: final / Resolution: 1.883→48.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 0 174 4790
Biso mean---37.01 -
Num. residues----572
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8838-1.92470.36811050.3296234076
1.9247-1.96940.3261480.311261886
1.9694-2.01860.3181380.318271689
2.0186-2.07320.37641200.3118275091
2.0732-2.13410.29861350.2986273491
2.1341-2.20290.3211640.2961276890
2.2029-2.28160.30281440.2791273291
2.2816-2.37280.35411200.2582282492
2.3728-2.48060.29011120.2631289894
2.4806-2.61120.31211460.2556280793
2.6112-2.77440.25671430.2361283694
2.7744-2.9880.23861570.2121286294
2.988-3.28770.21391620.183285894
3.2877-3.76090.22711300.146290595
3.7609-4.7290.17951570.1223289094
4.729-100.20861670.1492288694

+
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