› 9ca4

Electron Microscopy
3.01Å resolution

Human TOP3B-TDRD3 core complex in RNA rejoining state

Released:
DOI: 10.2210/pdb9ca4/pdb
PDB entry 9ca4 coloured by chain, front view.
PDB entry 9ca4 coloured by chain, side view.
PDB entry 9ca4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics.
Yang X, Chen X, Yang W, Pommier Y
Nat Commun 16 834 (2025)
PMID: 39828754
Related structures: EMD-45380

Function and Biology Details

Reaction catalysed: 
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-284875 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (4 distinct):
DNA topoisomerase 3-beta-1 Chain: A
Molecule details ›
Chain: A
Length: 612 amino acids
Theoretical weight: 69.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O95985 (Residues: 1-611; Coverage: 71%)
Gene names: TOP3B, TOP3B1
Sequence domains:
Tudor domain-containing protein 3 Chain: B
Molecule details ›
Chain: B
Length: 161 amino acids
Theoretical weight: 17.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H7E2 (Residues: 1-68; Coverage: 10%)
  • Best match: Q9H7E2-3 (Residues: 1-161)
Gene name: TDRD3
Sequence domains: RMI1, N-terminal OB-fold domain
RNA (5'-R(P*AP*CP*UP*AP*AP*A)-3') Chain: E
RNA (5'-R(*AP*U)-3') Chain: G

Ligands and Environments

1 bound ligand:
Ligand MN 2 x MN
1 modified residue:
Ligand PTR 1 x PTR

Experiments and Validation Details

Entry percentile scores
Resolution: 3.01Å
Relevant EMDB volumes: EMD-45380
Expression system: Homo sapiens

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