› 8t2r

Electron Microscopy
3.1Å resolution

Structure of a group II intron ribonucleoprotein in the pre-ligation (pre-2F) state

Released:
DOI: 10.2210/pdb8t2r/pdb
PDB entry 8t2r coloured by chain, front view.
PDB entry 8t2r coloured by chain, side view.
PDB entry 8t2r coloured by chain, top view.
Source organism: [Eubacterium] rectale
Primary publication:
Structural insights into intron catalysis and dynamics during splicing.
Xu L, Liu T, Chung K, Pyle AM
OpenAccess logo Nature (2023)
PMID: 37993708
Related structures: EMD-40985

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-249457 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Reverse transcriptase domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 427 amino acids
Theoretical weight: 49.08 KDa
Source organism: [Eubacterium] rectale
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A173ZME3 (Residues: 1-427; Coverage: 100%)
Gene names: ERS852417_00966, FYL37_05080, ltrA, ltrA_2
Sequence domains:
5'exon Chain: A
Molecule details ›
Chain: A
Length: 7 nucleotides
Theoretical weight: 2.1 KDa
Source organism: [Eubacterium] rectale
Expression system: Escherichia coli
Intron Chain: B
Molecule details ›
Chain: B
Length: 643 nucleotides
Theoretical weight: 208.4 KDa
Source organism: [Eubacterium] rectale
Expression system: Escherichia coli
Sequence domains:
  • Group II catalytic intron D1-D4-3
  • Group II catalytic intron D1-D4-1
  • Group II catalytic intron

    • Ligands and Environments

    2 bound ligands:
    Ligand CA 13 x CA
    Ligand NH4 2 x NH4
    No modified residues

    Experiments and Validation Details

    Entry percentile scores
    Resolution: 3.1Å
    Relevant EMDB volumes: EMD-40985
    Expression system: Escherichia coli

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