› 3mxh

X-ray diffraction
2.3Å resolution

Native structure of a c-di-GMP riboswitch from V. cholerae

Released:
DOI: 10.2210/pdb3mxh/pdb
PDB entry 3mxh coloured by chain, front view.
PDB entry 3mxh coloured by chain, side view.
PDB entry 3mxh coloured by chain, top view.
Source organisms:
Primary publication:
Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch .
Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA
Biochemistry 49 7351-9 (2010)
PMID: 20690679

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-140493 (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

2 bound ligands:
Ligand MG 5 x MG
Ligand C2E 1 x C2E
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: 50.243Å b: 45.652Å c: 80.248Å
α: 90° β: 93.74° γ: 90°
R-values:
R R work R free
0.203 0.202 0.239
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

12 review citations

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

19 mentions without citation

Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world.
Liberman et al. (2011)
18 more