3WO3

Crystal structure of IL-18 in complex with IL-18 receptor alpha

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 

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: 

    Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-18
A, C, E, G, I, K
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, D, F, H, J, L
312Homo sapiensMutation(s): 0 
Gene Names: IL18R1 (IL1RRP)
Find proteins for Q13478 (Homo sapiens)
Go to Gene View: IL18R1
Go to UniProtKB:  Q13478
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN
Download SDF File 
Download CCD File 
B, D, F, H
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC
Download SDF File 
Download CCD File 
B, D, F, H, J, L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA
Download SDF File 
Download CCD File 
B, D, F, H, J, L
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, D, F, H, J, L
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: 0.222 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.490α = 90.00
b = 174.814β = 90.00
c = 183.398γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BSSdata collection
SCALAdata scaling
BUSTERrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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