› 6t3s

X-ray diffraction
3.28Å resolution

Structure of Oceanobacillus iheyensis group II intron U-mutant (C289U/C358U/G385A) in the presence of Na+, Mg2+ and 5'-exon

Released:
DOI: 10.2210/pdb6t3s/pdb
Model geometry
Fit model/data
PDB entry 6t3s coloured by chain, front view.
PDB entry 6t3s coloured by chain, side view.
PDB entry 6t3s 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
OpenAccess logo 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:
monomeric (preferred)
PDBe Complex ID:
PDB-CPX-303326 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
Group IIC Intron Ribozyme Chain: A
Molecule details ›
Chain: A
Length: 398 nucleotides
Theoretical weight: 129.23 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

    • Ligands and Environments

    3 bound ligands:
    Ligand MG 20 x MG
    Ligand NA 8 x NA
    Ligand EPE 3 x EPE
    No modified residues

    Experiments and Validation Details

    wwPDB Validation report is not available for this entry.
    X-ray source: APS BEAMLINE 24-ID-C
    Spacegroup: P212121
    Unit cell:
    a: 89.89Å b: 95.24Å c: 227.896Å
    α: 90° β: 90° γ: 90°
    R-values:
    R R work R free
    0.198 0.197 0.23
    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)