› 3wo4

X-ray diffraction
3.1Å resolution

Crystal structure of the IL-18 signaling ternary complex

Released:
DOI: 10.2210/pdb3wo4/pdb
PDB entry 3wo4 coloured by chain, front view.
PDB entry 3wo4 coloured by chain, side view.
PDB entry 3wo4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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 EY, Kondo N, Shirakawa M, Tochio H, Kato Z
Nat Commun 5 5340 (2014)
PMID: 25500532

Function and Biology Details

Reaction catalysed: 
(1a) NAD(+) = cyclic ADP-ribose + nicotinamide
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-131868 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (9 distinct):
Interleukin-18 Chain: A
Molecule details ›
Chain: A
Length: 157 amino acids
Theoretical weight: 18.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q14116 (Residues: 37-193; Coverage: 81%)
Gene names: IGIF, IL18, IL1F4
Sequence domains: Interleukin-1 / 18
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Interleukin-18 receptor 1 Chain: B
Molecule details ›
Chain: B
Length: 312 amino acids
Theoretical weight: 35.9 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13478 (Residues: 20-329; Coverage: 59%)
Gene names: IL18R1, IL1RRP
Structure domains: Immunoglobulins
Interleukin-18 receptor accessory protein Chain: C
Molecule details ›
Chain: C
Length: 344 amino acids
Theoretical weight: 39.24 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O95256 (Residues: 15-356; Coverage: 58%)
Gene names: IL18RAP, IL1R7
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand NAG 3 x NAG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: P212121
Unit cell:
a: 72.56Å b: 111.56Å c: 134.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.232
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

21 review citations

Overview of the IL-1 family in innate inflammation and acquired immunity.
Dinarello CA. (2018)
20 more

15 mentions without citation

Structural Basis of IL-1 Family Cytokine Signaling.
Fields et al. (2019)
14 more