› 4kze

X-ray diffraction
2.4Å resolution

Crystal structure of an RNA aptamer in complex with Fab

Released:
DOI: 10.2210/pdb4kze/pdb
PDB entry 4kze coloured by chain, front view.
PDB entry 4kze coloured by chain, side view.
PDB entry 4kze coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA
Nat Chem Biol 10 686-91 (2014)
PMID: 24952597

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
monomeric
PDBe Complex ID:
PDB-CPX-212925 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
BL3-6 Fab antibody, heavy chain Chain: H
Molecule details ›
Chain: H
Length: 232 amino acids
Theoretical weight: 24.67 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
BL3-6 Fab antibody, light chain Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.39 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
RNA (84-MER) Chain: R
Molecule details ›
Chain: R
Length: 84 nucleotides
Theoretical weight: 27.45 KDa

Ligands and Environments

2 bound ligands:
Ligand K 1 x K
Ligand MG 1 x MG
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2
Unit cell:
a: 146.941Å b: 80.104Å c: 94.519Å
α: 90° β: 111.86° γ: 90°
R-values:
R R work R free
0.188 0.186 0.224
Expression system: Escherichia coli

Quick links

Citations

29 review citations

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms.
Fay et al. (2017)
28 more

7 mentions without citation

Selection and Biosensor Application of Aptamers for Small Molecules.
Pfeiffer et al. (2016)
6 more