› 3irw

X-ray diffraction
2.7Å resolution

Structure of a c-di-GMP riboswitch from V. cholerae

Released:
DOI: 10.2210/pdb3irw/pdb
PDB entry 3irw coloured by chain, front view.
PDB entry 3irw coloured by chain, side view.
PDB entry 3irw coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of ligand binding by a c-di-GMP riboswitch.
Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA
Nat Struct Mol Biol 16 1218-23 (2009)
PMID: 19898477

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-140487 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 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
c-di-GMP Riboswitch 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

Ligands and Environments

3 bound ligands:
Ligand C2E 1 x C2E
Ligand IRI 9 x IRI
Ligand MG 2 x MG
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21
Unit cell:
a: 49.461Å b: 45.123Å c: 76.573Å
α: 90° β: 96.79° γ: 90°
R-values:
R R work R free
0.199 0.196 0.251
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

42 review citations

Prospects for riboswitch discovery and analysis.
Breaker RR. (2011)
41 more

29 mentions without citation

Cyclic di-GMP: the first 25 years of a universal bacterial second messenger.
Römling et al. (2013)
28 more