› 4yb1

X-ray diffraction
2.08Å resolution

20A Mutant c-di-GMP Vc2 Riboswitch bound with 3',3'-cGAMP

Released:
DOI: 10.2210/pdb4yb1/pdb
PDB entry 4yb1 coloured by chain, front view.
PDB entry 4yb1 coloured by chain, side view.
PDB entry 4yb1 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch.
Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ
Cell Rep 11 1-12 (2015)
PMID: 25818298

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-140504 (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: 92 amino acids
Theoretical weight: 10.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P09012 (Residues: 7-97; Coverage: 32%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
RNA (91-MER) Chain: R
Molecule details ›
Chain: R
Length: 91 nucleotides
Theoretical weight: 29.46 KDa
Source organism: Vibrio cholerae
Expression system: in vitro transcription vector pT7-Fluc(deltai)
Sequence domains: Cyclic di-GMP-I riboswitch

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand 4BW 1 x 4BW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 51.738Å b: 46.836Å c: 80.791Å
α: 90° β: 90.44° γ: 90°
R-values:
R R work R free
0.222 0.218 0.298
Expression systems:
  • Escherichia coli BL21
  • in vitro transcription vector pT7-Fluc(deltai)

Quick links

Citations

7 review citations

Maximising the potential of AKT inhibitors as anti-cancer treatments.
Brown et al. (2017)
6 more

10 mentions without citation

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