› 4qln

X-ray diffraction
2.65Å resolution

structure of ydao riboswitch binding with c-di-dAMP

Released:
DOI: 10.2210/pdb4qln/pdb
PDB entry 4qln coloured by chain, front view.
PDB entry 4qln coloured by chain, side view.
PDB entry 4qln coloured by chain, top view.
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Primary publication:
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets.
Ren A, Patel DJ
Nat Chem Biol 10 780-6 (2014)
PMID: 25086509

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195881 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
RNA (117-MER) Chain: A
Molecule details ›
Chain: A
Length: 125 nucleotides
Theoretical weight: 40.51 KDa
Source organism: Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression system: Not provided
Sequence domains: ydaO/yuaA leader

Ligands and Environments

2 bound ligands:
Ligand 2BA 2 x 2BA
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2221
Unit cell:
a: 77.874Å b: 87.051Å c: 144.553Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.217 0.29
Expression system: Not provided

Quick links

Citations

18 review citations

RNA Structure: Advances and Assessment of 3D Structure Prediction.
Miao et al. (2017)
17 more

7 mentions without citation

Cyclic di-AMP, a second messenger of primary importance: tertiary structures and binding mechanisms.
He et al. (2020)
6 more