› 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 entry 4q9q coloured by chain, front view.
PDB entry 4q9q coloured by chain, side view.
PDB entry 4q9q 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

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-212926 (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

28 review citations

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

11 mentions without citation

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