› 6t3k

X-ray diffraction
3.44Å resolution

Structure of Oceanobacillus iheyensis group II intron G-mutant (C289G/C358G/G385C) in the presence of K+, Mg2+ and 5'-exon

Released:
DOI: 10.2210/pdb6t3k/pdb
PDB entry 6t3k coloured by chain, front view.
PDB entry 6t3k coloured by chain, side view.
PDB entry 6t3k coloured by chain, top view.
Source organism: Oceanobacillus iheyensis
Primary publication:
Visualizing group II intron dynamics between the first and second steps of splicing.
Manigrasso J, Chillón I, Genna V, Vidossich P, Somarowthu S, Pyle AM, De Vivo M, Marcia M
Nat Commun 11 2837 (2020)
PMID: 32503992

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-195928 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
Group IIC Intron Ribozyme Chain: A
Molecule details ›
Chain: A
Length: 390 nucleotides
Theoretical weight: 126.65 KDa
Source organism: Oceanobacillus iheyensis
Expression system: Not provided
Sequence domains:
  • Group II catalytic intron D1-D4-3
  • Group II catalytic intron D1-D4-1
    • Group IIC Intron Ribozyme Chain: B
    Molecule details ›
    Chain: B
    Length: 8 nucleotides
    Theoretical weight: 2.58 KDa
    Source organism: Oceanobacillus iheyensis
    Expression system: Not provided

    Ligands and Environments

    4 bound ligands:
    Ligand MG 28 x MG
    Ligand K 15 x K
    Ligand EPE 5 x EPE
    Ligand SPM 2 x SPM
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    X-ray source: APS BEAMLINE 24-ID-C
    Spacegroup: P212121
    Unit cell:
    a: 88.659Å b: 95.453Å c: 224.978Å
    α: 90° β: 90° γ: 90°
    R-values:
    R R work R free
    0.212 0.209 0.257
    Expression system: Not provided

    Quick links

    Citations

    3 review citations

    Noncoding RNAs: biology and applications-a Keystone Symposia report.
    Cable et al. (2021)
    2 more

    1 mention without citation

    Visualizing group II intron dynamics between the first and second steps of splicing.
    Manigrasso et al. (2020)