› 8wt8

Electron Microscopy
2.9Å resolution

Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, donor DNA, and target DNA in the post-strand exchange state (Holliday junction intermediate)

Released:
DOI: 10.2210/pdb8wt8/pdb
PDB entry 8wt8 coloured by chain, front view.
PDB entry 8wt8 coloured by chain, side view.
PDB entry 8wt8 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural mechanism of bridge RNA-guided recombination.
Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H
OpenAccess logo Nature 630 994-1002 (2024)
PMID: 38926616
Related structures: EMD-37829

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-246144 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (6 distinct):
IS621, transposase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 328 amino acids
Theoretical weight: 36.74 KDa
Source organism: Escherichia coli
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: A0A2X3M8B0 (Residues: 17-342; Coverage: 95%)
Gene name: NCTC8009_08584
Sequence domains:
target DNA-donor DNA Chain: G
Molecule details ›
Chain: G
Length: 49 nucleotides
Theoretical weight: 15 KDa
Source organism: Escherichia coli
Expression system: Not provided
target DNA Chain: H
Molecule details ›
Chain: H
Length: 38 nucleotides
Theoretical weight: 11.7 KDa
Source organism: Escherichia coli
Expression system: Not provided
donor DNA-target DNA Chain: I
Molecule details ›
Chain: I
Length: 33 nucleotides
Theoretical weight: 10.16 KDa
Source organism: Escherichia coli
Expression system: Not provided
donor DNA Chain: J
Molecule details ›
Chain: J
Length: 44 nucleotides
Theoretical weight: 13.59 KDa
Source organism: Escherichia coli
Expression system: Not provided
bridge RNA Chains: E, F
Molecule details ›
Chains: E, F
Length: 180 nucleotides
Theoretical weight: 57.67 KDa
Source organism: Escherichia coli
Expression system: synthetic construct

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-37829
Expression systems:
  • Spodoptera frugiperda
  • Not provided
  • synthetic construct

Quick links