[English] 日本語
Yorodumi
- PDB-7al7: The Crystal Structure of Human IL-18 in Complex With Human IL-18 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7al7
TitleThe Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
Components
  • Glutathione S-transferase class-mu 26 kDa isozyme,Interleukin-18
  • Interleukin-18-binding protein
KeywordsCYTOKINE / decoy receptor / antagonist / complex
Function / homology
Function and homology information


interleukin-18 binding / interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / receptor antagonist activity / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway ...interleukin-18 binding / interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / receptor antagonist activity / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 1 cell cytokine production / positive regulation of macrophage derived foam cell differentiation / positive regulation of neuroinflammatory response / interleukin-18-mediated signaling pathway / positive regulation of interleukin-13 production / natural killer cell mediated cytotoxicity / negative regulation of myoblast differentiation / type 2 immune response / natural killer cell activation / neutrophil activation / sleep / Interleukin-1 processing / positive regulation of NK T cell proliferation / Interleukin-37 signaling / triglyceride homeostasis / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of natural killer cell proliferation / T-helper 1 type immune response / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / Interleukin-10 signaling / glutathione transferase / glutathione transferase activity / establishment of skin barrier / Pyroptosis / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cytokine activity / cholesterol homeostasis / positive regulation of smooth muscle cell proliferation / cellular response to hydrogen peroxide / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / cell-cell signaling / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / positive regulation of NF-kappaB transcription factor activity / Interleukin-4 and Interleukin-13 signaling / angiogenesis / cellular response to lipopolysaccharide / cell population proliferation / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / defense response to Gram-positive bacterium / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Interleukin-18-binding protein / Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. ...Interleukin-18-binding protein / Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Interleukin-18-binding protein / Glutathione S-transferase class-mu 26 kDa isozyme / Interleukin-18
Similarity search - Component
Biological speciesHomo sapiens (human)
Schistosoma japonicum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsDetry, S. / Andries, J. / Bloch, Y. / Clancy, D. / Savvides, S.N.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)779295European Union
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis of human IL-18 sequestration by the decoy receptor IL-18 binding protein in inflammation and tumor immunity.
Authors: Detry, S. / Andries, J. / Bloch, Y. / Gabay, C. / Clancy, D.M. / Savvides, S.N.
History
DepositionOct 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 25, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Jan 31, 2024Group: 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-binding protein
B: Glutathione S-transferase class-mu 26 kDa isozyme,Interleukin-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1095
Polymers64,4452
Non-polymers6643
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-3 kcal/mol
Surface area13650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.815, 44.520, 60.276
Angle α, β, γ (deg.)90.000, 99.860, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Interleukin-18-binding protein / IL-18BP / Tadekinig-alfa


Mass: 18749.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The final protein sequence used for crystallization starts at T30 and ends at D170. The N-terminal RTPmu signal sequence is cleaved during expression. The C-terminal AVI-HIS tag was cleaved ...Details: The final protein sequence used for crystallization starts at T30 and ends at D170. The N-terminal RTPmu signal sequence is cleaved during expression. The C-terminal AVI-HIS tag was cleaved by caspase-3 after the DEVD site. In reference to the native sequence, the final protein sequence starts at Q63 and ends at G194, as it lacks an N-terminal region from T31 to K62.
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18BP / Plasmid: pHLSec / Cell line (production host): HEK293S MGAT -/- / Production host: Homo sapiens (human) / References: UniProt: O95998
#2: Protein Glutathione S-transferase class-mu 26 kDa isozyme,Interleukin-18 / GST 26 / Sj26 antigen / SjGST / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma- ...GST 26 / Sj26 antigen / SjGST / IL-18 / Iboctadekin / Interferon gamma-inducing factor / IFN-gamma-inducing factor / Interleukin-1 gamma / IL-1 gamma


Mass: 45695.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at ...Details: The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193,The protein was expressed as a HIS-GST fusion which was cleaved after the DEVD site using caspasea-3. Thus, the final protein sequence used for crystallization starts at Y234 and ends at D390. In reference to the native sequence, the final protein sequence starts at Y37 and ends at D193
Source: (gene. exp.) Schistosoma japonicum (invertebrata), (gene. exp.) Homo sapiens (human)
Plasmid: pET-42 / Gene: IL18, IGIF, IL1F4 / Details (production host): HIS-GST tag added N-terminally / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P08515, UniProt: Q14116, glutathione transferase
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 18% w/v Polyethylene glycol 8000
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→59.39 Å / Num. obs: 26507 / % possible obs: 98.27 % / Redundancy: 6.9 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 15.67
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.8-1.911.7541790.9481.063197.6
1.91-2.043.4639990.9780.526198.3
2.04-2.25.737340.9910.3199
2.2-2.418.8634480.9960.18199.4
2.41-2.712.8134480.9970.12199.2
2.7-3.1222.1527640.9990.063199
3.12-3.8137.6823510.9990.09199.7
3.81-5.3851.0718510.9990.031199
5.38-59.3955.6210500.9993.2199

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACTv3.25data extraction
XDSvMar 15, 2019data reduction
XSCALEvMar 15, 2019data scaling
PHASERv2.8phasing
STARANISOv1.0.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F62

3f62


Resolution: 1.801→59.386 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 2640 10.01 %random
Rwork0.2088 23728 --
obs0.2111 26368 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.21 Å2 / Biso mean: 38.4789 Å2 / Biso min: 5.01 Å2
Refinement stepCycle: final / Resolution: 1.801→59.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2113 0 84 130 2327
Biso mean--72.95 35.18 -
Num. residues----265
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.801-1.83330.58711350.5534118395
1.8333-1.86860.59281250.5089123097
1.8686-1.90680.46811460.4576121297
1.9068-1.94820.46291370.371124098
1.9482-1.99350.40141330.3382121997
1.9935-2.04340.37781310.3248125598
2.0434-2.09860.37531360.3143122798
2.0986-2.16040.32451460.3006124398
2.1604-2.23010.33411460.2821123198
2.2301-2.30980.28891330.276123799
2.3098-2.40230.34241270.2536128999
2.4023-2.51170.31231560.2509123899
2.5117-2.64410.28471360.2298125699
2.6441-2.80970.22771340.2159125899
2.8097-3.02670.21531420.2166126499
3.0267-3.33120.19871510.1881255100
3.3312-3.81320.20461340.17641285100
3.8132-4.80390.16221430.1321129199
4.8039-59.3860.17791490.1809131599

+
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