› 4q9q

X-ray diffraction
2.45Å resolution

Crystal structure of an RNA aptamer bound to bromo-ligand analog in complex with Fab

Released:
DOI: 10.2210/pdb4q9q/pdb
PDB 4q9q coloured by chain and viewed from the front.
PDB 4q9q coloured by chain and viewed from the side.
PDB 4q9q coloured by chain and viewed from the top.
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. (2014)
PMID: 24952597

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (3 distinct):
Fab BL3-6, HEAVY CHAIN Chain: H
Molecule details ›
Chain: H
Length: 225 amino acids
Theoretical weight: 23.85 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab BL3-6, 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
Spinach RNA aptamer Chain: R
Molecule details ›
Chain: R
Length: 84 nucleotides
Theoretical weight: 27.37 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand K 1 x K
Ligand 2ZZ 1 x 2ZZ
1 modified residue:
Ligand GDP 1 x GDP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: C2
Unit cell:
a: 146.545Å b: 79.676Å c: 95.28Å
α: 90° β: 111.51° γ: 90°
R-values:
R R work R free
0.184 0.182 0.22
Expression system: Escherichia coli

Quick links

Citations

25 review citations

Recent advances in RNA structurome.
Xu et al. (2022)
24 more

11 mentions without citation

RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers.
Neubacher et al. (2019)
10 more