Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 9c9w
Q-score: 0.198
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Dna (5'-d(*ap*tp*tp*gp*gp*ap*gp*tp*tp*cp*ap*tp*gp*tp*gp*ap*tp*gp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (38-mer) (12 kDa, DNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(p*cp*ap*gp*ap*tp*cp*ap*gp*ap*ap*tp*gp*ap*ap*tp*ap*tp*ap*cp*tp*ap*ap*a)-3') (7 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dimerized human top3b-tdrd3 core complexes with a dna mismatch bubble (Complex from Homo sapiens)
Human TOP3B-TDRD3 core complex in RNA rejoining state
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 9ca4
Q-score: 0.451
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with rna (Complex from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Rna (5'-r(p*ap*cp*up*ap*ap*a)-3') (1 kDa, RNA from Homo sapiens)
- Rna (5'-r(*ap*u)-3') (590 Da, RNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
Human TOP3B-TDRD3 core complex in RNA pre-cleavage state
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 9cag
Q-score: 0.483
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with rna (Complex from Homo sapiens)
- Rna (5'-r(p*ap*cp*up*ap*ap*ap*ap*u)-3') (2 kDa, RNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
Resolution: 3.16 Å
EM Method: Single-particle
Fitted PDBs: 9cah
Q-score: 0.475
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Zinc ion (65 Da, Ligand)
- Dna topoisomerase 3-beta-1 (81 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 complex (Complex from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Tudor domain-containing protein 3 (20 kDa, Protein from Homo sapiens)
Human TOP3B-TDRD3 core complex in pre-cleavage state with ssDNA 5'-ACAGATATT-3
Resolution: 3.51 Å
EM Method: Single-particle
Fitted PDBs: 9caj
Q-score: 0.443
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with dna (Complex from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(p*ap*cp*ap*gp*ap*tp*ap*tp*t)-3') (2 kDa, DNA from Homo sapiens)
Human TOP3B-TDRD3 core complex in DNA rejoining state with ssDNA 5'-GACAGATATT-3
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 9cak
Q-score: 0.517
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with dna (Complex from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*gp*ap*cp*ap*gp*ap*t)-3') (2 kDa, DNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(*ap*tp*t)-3') (876 Da, DNA from Homo sapiens)
Human TOP3B-TDRD3 core complex in post-cleavage state with ssDNA 5'-ACAGATATT-3
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 9cal
Q-score: 0.506
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with ssdna (Complex from Homo sapiens)
- Dna (5'-d(p*gp*ap*cp*ap*gp*ap*t)-3') (2 kDa, DNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(*ap*tp*t)-3') (876 Da, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
Human TOP3B-TDRD3 core complex in DNA pre-cleavage state
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 9c9y
Q-score: 0.467
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with dna (Complex from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(p*ap*cp*tp*ap*ap*ap*ap*t)-3') (2 kDa, DNA from Homo sapiens)
Human TOP3B-TDRD3 core complex in DNA post-cleavage state
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 9ca0
Q-score: 0.455
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with dna (Complex from Homo sapiens)
- Dna (5'-d(p*tp*ap*cp*tp*ap*ap*a)-3') (2 kDa, DNA from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(*ap*tp*t)-3') (876 Da, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
Human TOP3B-TDRD3 core complex in DNA religation state
Resolution: 3.26 Å
EM Method: Single-particle
Fitted PDBs: 9ca1
Q-score: 0.478
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Human top3b-tdrd3 core complex with dna (Complex from Homo sapiens)
- Dna (5'-d(p*tp*ap*cp*tp*ap*ap*a)-3') (2 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Manganese (ii) ion (54 Da, Ligand)
- Dna (5'-d(*ap*tp*t)-3') (876 Da, DNA from Homo sapiens)