› 4e8t

X-ray diffraction
3.34Å resolution

Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Ca2+ and an oligonucleotide fragment substrate (low energy dataset)

Released:
DOI: 10.2210/pdb4e8t/pdb
PDB entry 4e8t coloured by chain, front view.
PDB entry 4e8t coloured by chain, side view.
PDB entry 4e8t coloured by chain, top view.
Source organism: Oceanobacillus iheyensis
Primary publication:
Visualizing group II intron catalysis through the stages of splicing.
Marcia M, Pyle AM
Cell 151 497-507 (2012)
PMID: 23101623

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-195924 (preferred)
Entry contents:
2 distinct RNA molecules
Macromolecules (2 distinct):
Group IIC intron Chain: A
Molecule details ›
Chain: A
Length: 393 nucleotides
Theoretical weight: 127.65 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
    • 5'-R(*AP*UP*UP*UP*AP*UP*UP*A)-3' Chain: B
    Molecule details ›
    Chain: B
    Length: 8 nucleotides
    Theoretical weight: 2.47 KDa
    Source organism: Oceanobacillus iheyensis
    Expression system: Not provided

    Ligands and Environments

    4 bound ligands:
    Ligand CA 25 x CA
    Ligand K 14 x K
    Ligand SPM 2 x SPM
    Ligand EPE 6 x EPE
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    X-ray source: APS BEAMLINE 24-ID-C
    Spacegroup: P212121
    Unit cell:
    a: 88.458Å b: 95.765Å c: 225.688Å
    α: 90° β: 90° γ: 90°
    R-values:
    R R work R free
    0.191 0.189 0.235
    Expression system: Not provided

    Quick links

    Citations

    29 review citations

    Mechanisms and Regulation of Alternative Pre-mRNA Splicing.
    Lee et al. (2015)
    28 more

    2 mentions without citation

    Visualizing group II intron catalysis through the stages of splicing.
    Marcia et al. (2012)
    1 more