› 4w90

X-ray diffraction
3.12Å resolution

Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO

Released:
DOI: 10.2210/pdb4w90/pdb
PDB entry 4w90 coloured by chain, front view.
PDB entry 4w90 coloured by chain, side view.
PDB entry 4w90 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.
Jones CP, Ferré-D'Amaré AR
EMBO J 33 2692-703 (2014)
PMID: 25271255

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140502 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chain: B
Molecule details ›
Chain: B
Length: 91 amino acids
Theoretical weight: 10.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P09012 (Residues: 6-96; Coverage: 32%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
riboswitch a pseudo-dimeric RNA Chain: C
Molecule details ›
Chain: C
Length: 119 nucleotides
Theoretical weight: 38.3 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
Sequence domains: ydaO/yuaA leader

Ligands and Environments

2 bound ligands:
Ligand 2BA 2 x 2BA
Ligand MG 5 x MG
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: I222
Unit cell:
a: 59.28Å b: 84.85Å c: 230.536Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.236 0.23 0.288
Expression system: Escherichia coli

Quick links

Citations

6 review citations

A jack of all trades: the multiple roles of the unique essential second messenger cyclic di-AMP.
Commichau et al. (2015)
5 more

7 mentions without citation

A decade of research on the second messenger c-di-AMP.
Yin et al. (2020)
6 more