› 4gaf

X-ray diffraction
2.15Å resolution

Crystal structure of EBI-005, a chimera of human IL-1beta and IL-1Ra, bound to human Interleukin-1 receptor type 1

Released:
DOI: 10.2210/pdb4gaf/pdb
PDB entry 4gaf coloured by chain, front view.
PDB entry 4gaf coloured by chain, side view.
PDB entry 4gaf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design of a superior cytokine antagonist for topical ophthalmic use.
Hou J, Townson SA, Kovalchin JT, Masci A, Kiner O, Shu Y, King BM, Schirmer E, Golden K, Thomas C, Garcia KC, Zarbis-Papastoitsis G, Furfine ES, Barnes TM
Proc Natl Acad Sci U S A 110 3913-8 (2013)
PMID: 23431173

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-134410 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Interleukin-1 beta Chain: A
Molecule details ›
Chain: A
Length: 153 amino acids
Theoretical weight: 17.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01584 (Residues: 117-255, 256-269; Coverage: 57%)
Gene names: IL1B, IL1F2
Sequence domains: Interleukin-1 / 18
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Interleukin-1 receptor type 1, soluble form Chain: B
Molecule details ›
Chain: B
Length: 319 amino acids
Theoretical weight: 36.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14778 (Residues: 18-336; Coverage: 58%)
Gene names: IL1R, IL1R1, IL1RA, IL1RT1
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand NAG 4 x NAG
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2221
Unit cell:
a: 60.35Å b: 149.27Å c: 126.17Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.218 0.216 0.271
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Structural biology of the IL-1 superfamily: key cytokines in the regulation of immune and inflammatory responses.
Krumm et al. (2014)
10 more

12 mentions without citation

The Therapeutic Prospects of Targeting IL-1R1 for the Modulation of Neuroinflammation in Central Nervous System Disorders.
Luís et al. (2022)
11 more