› 6dg5

X-ray diffraction
2.52Å resolution

Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg

Released:
DOI: 10.2210/pdb6dg5/pdb
PDB entry 6dg5 coloured by chain, front view.
PDB entry 6dg5 coloured by chain, side view.
PDB entry 6dg5 coloured by chain, top view.
Source organisms:
Primary publication:
De novo design of potent and selective mimics of IL-2 and IL-15.
Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJL, Dougan M, Garcia KC, Baker D
Nature 565 186-191 (2019)
PMID: 30626941

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-147676 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
Neoleukin-2/15 Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 12.11 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
Interleukin-2 receptor subunit beta Chain: B
Molecule details ›
Chain: B
Length: 209 amino acids
Theoretical weight: 24.47 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P16297 (Residues: 27-235; Coverage: 41%)
Gene name: Il2rb
Sequence domains: Interleukin-2 receptor subunit beta N-terminal domain 1
Structure domains: Immunoglobulins
Cytokine receptor common subunit gamma Chain: C
Molecule details ›
Chain: C
Length: 199 amino acids
Theoretical weight: 23.8 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P34902 (Residues: 56-254; Coverage: 57%)
Gene name: Il2rg
Sequence domains:
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Unit cell:
a: 65.125Å b: 67.914Å c: 172.084Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.221 0.266
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

69 review citations

Recent advances and discoveries in the mechanisms and functions of CAR T cells.
Larson et al. (2021)
68 more

4 mentions without citation

De novo design of potent and selective mimics of IL-2 and IL-15.
Silva et al. (2019)
3 more