› 5uc6

X-ray diffraction
2.1Å resolution

Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III

Released:
DOI: 10.2210/pdb5uc6/pdb
PDB entry 5uc6 coloured by chain, front view.
PDB entry 5uc6 coloured by chain, side view.
PDB entry 5uc6 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling.
Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM
Nat Commun 8 810 (2017)
PMID: 28993621

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119206 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Interleukin-1 alpha Chain: A
Molecule details ›
Chain: A
Length: 159 amino acids
Theoretical weight: 18.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01583 (Residues: 113-271; Coverage: 59%)
Gene names: IL1A, IL1F1
Sequence domains: Interleukin-1 / 18
Structure domains: Trefoil (Acidic Fibroblast Growth Factor, subunit A)
DNA (5'-D(*CP*G)-R(P*(85Y))-D(P*GP*AP*G)-R(P*(85Y)P*(85Y))-D(P*A)-R(P*(85Y))-D(P*GP*GP*G)-R(P*(85Y)P*(85Y))-D(P*AP*GP*AP*G)-R(P*(85Y))-D(P*CP*GP*(ATD))-3') Chain: B
Molecule details ›
Chain: B
Length: 23 nucleotides
Theoretical weight: 8.37 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand NA 1 x NA
Ligand PO4 1 x PO4
2 modified residues:
Ligand 85Y 7 x 85Y
Ligand ATD 1 x ATD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3121
Unit cell:
a: 74.79Å b: 74.79Å c: 86.36Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.178 0.219
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

10 review citations

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

8 mentions without citation

Structural Biology for the Molecular Insight between Aptamers and Target Proteins.
Zhang et al. (2021)
7 more