› 3wo3

X-ray diffraction
3.1Å resolution

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

Released:
DOI: 10.2210/pdb3wo3/pdb
PDB entry 3wo3 coloured by chain, front view.
PDB entry 3wo3 coloured by chain, side view.
PDB entry 3wo3 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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171711 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (11 distinct):
Interleukin-18 Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
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 Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
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

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
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC, BMA, MAN
Carbohydrate polymer
2 bound ligands:
Ligand SO4 38 x SO4
Ligand NAG 8 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 135.49Å b: 174.814Å c: 183.398Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.222
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

12 mentions without citation

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