› 3ud4

X-ray diffraction
2.7Å resolution

The C92U mutant c-di-GMP-I riboswitch bound to GpA

Released:
DOI: 10.2210/pdb3ud4/pdb
PDB entry 3ud4 coloured by chain, front view.
PDB entry 3ud4 coloured by chain, side view.
PDB entry 3ud4 coloured by chain, top view.
Source organisms:
Primary publication:
Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.
Smith KD, Lipchock SV, Strobel SA
Biochemistry 51 425-32 (2012)
PMID: 22148472

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140499 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
U1 small nuclear ribonucleoprotein A Chain: P
Molecule details ›
Chain: P
Length: 98 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P09012 (Residues: 1-98; Coverage: 35%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
RNA (92-MER) Chain: R
Molecule details ›
Chain: R
Length: 92 nucleotides
Theoretical weight: 29.94 KDa
Source organism: Vibrio cholerae
Expression system: Not provided
Sequence domains: Cyclic di-GMP-I riboswitch
RNA (5'-R(*GP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 2 nucleotides
Theoretical weight: 629 Da
Source organism: Vibrio cholerae
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 49.612Å b: 45.116Å c: 76.049Å
α: 90° β: 96.05° γ: 90°
R-values:
R R work R free
0.225 0.222 0.29
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

8 review citations

Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis.
Kalia et al. (2013)
7 more

4 mentions without citation

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools.
Antunes et al. (2017)
3 more