3WO4

Crystal structure of the IL-18 signaling ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structural basis for receptor recognition of human interleukin-18

Tsutsumi, N.Kimura, T.Arita, K.Ariyoshi, M.Ohnishi, H.Yamamoto, T.Zuo, X.Maenaka, K.Park, E.Y.Kondo, N.Shirakawa, M.Tochio, H.Kato, Z.

(2014) Nat Commun 5: 5340-5340

  • DOI: 10.1038/ncomms6340
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Interleukin (IL)-18 is a proinflammatory cytokine that belongs to the IL-1 family and plays an important role in inflammation. The uncontrolled release of this cytokine is associated with severe chronic inflammatory disease. IL-18 forms a signalling ...

    Interleukin (IL)-18 is a proinflammatory cytokine that belongs to the IL-1 family and plays an important role in inflammation. The uncontrolled release of this cytokine is associated with severe chronic inflammatory disease. IL-18 forms a signalling complex with the IL-18 receptor α (Rα) and β (Rβ) chains at the plasma membrane, which induces multiple inflammatory cytokines. Here, we present a crystal structure of human IL-18 bound to the two receptor extracellular domains. Generally, the receptors' recognition mode for IL-18 is similar to IL-1β; however, certain notable differences were observed. The architecture of the IL-18 receptor second domain (D2) is unique among the other IL-1R family members, which presumably distinguishes them from the IL-1 receptors that exhibit a more promiscuous ligand recognition mode. The structures and associated biochemical and cellular data should aid in developing novel drugs to neutralize IL-18 activity.


    Organizational Affiliation

    Research Institute of Green Science and Technology, Department of Bioscience, Graduate school of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan.,Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.,X-Ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA.,1] Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan [2] Heisei College of Health Sciences, 180 Kurono, Gifu 501-1131, Japan.,Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045, Japan.,Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8502, Japan.,1] Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan [2] Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan.,1] Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan [2] Biomedical Informatics, Medical Information Sciences Division, The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1194, Japan.,1] Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan [2] Core Research of Evolution Science (CREST), Japan Sciences and Technology Agency, Tokyo 102-0076, Japan.,Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, , Kita-12, Nishi-6, Kita-ki, Sapporo 060-0812, Japan.,Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-18
A
157Homo sapiensMutation(s): 0 
Gene Names: IL18 (IGIF, IL1F4)
Find proteins for Q14116 (Homo sapiens)
Go to Gene View: IL18
Go to UniProtKB:  Q14116
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-18 receptor 1
B
312Homo sapiensMutation(s): 0 
Gene Names: IL18R1 (IL1RRP)
Find proteins for Q13478 (Homo sapiens)
Go to Gene View: IL18R1
Go to UniProtKB:  Q13478
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-18 receptor accessory protein
C
344Homo sapiensMutation(s): 0 
Gene Names: IL18RAP (IL1R7)
Find proteins for O95256 (Homo sapiens)
Go to Gene View: IL18RAP
Go to UniProtKB:  O95256
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.560α = 90.00
b = 111.560β = 90.00
c = 134.560γ = 90.00
Software Package:
Software NamePurpose
UGUISdata collection
PHASERphasing
HKL-2000data scaling
BUSTERrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2016-01-20
    Type: Database references