Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7i
Q-score: 0.443
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8x7j
Q-score: 0.391
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Rnf168/ubch5c-ub/nucleosomes complex determined by activity-based chemical trapping strategy (Complex from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 3.27 Å
EM Method: Single-particle
Fitted PDBs: 8x7k
Q-score: 0.423
Ai H, Tong Z, Deng Z, Shi Q, Tao S, Liang J, Sun M, Wu X, Zheng Q, Liang L, Li JB, Gao S, Tian C, Liu L, Pan M
bioRxiv (2024) [ DOI: doi:10.1101/2024.01.02.573964 ]
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Cryo-em structures of rnf168/ubch5c-ub in complex with h2ak13ub nucleosomes determined by activity-based chemical trapping strategy (adjacent h2ak13/15 dual-monoubiquitination) (Complex from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA from Homo sapiens)
Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8wg5
Q-score: 0.306
Ai H, He Z, Deng Z, Chu GC, Shi Q, Tong Z, Li JB, Pan M, Liu L
Nat Struct Mol Biol (2024) 31 pp. 1745-1755 [ Pubmed: 38918638 DOI: doi:10.1038/s41594-024-01342-2 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Ubiquitin b (8 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Complex of usp16 bound to h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 16 (93 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8hqy
Q-score: 0.47
Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L
Nat Struct Mol Biol (2024) 31 pp. 300-310 [ DOI: doi:10.1038/s41594-023-01141-1 Pubmed: 38177667 ]
- Dna (137-mer) (41 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Ssx1-h2ak119ub nucleosome complex (290 kDa, Complex from Homo sapiens)
- Histone h4 (fragment) (9 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (fragment) (8 kDa, Protein from Homo sapiens)
- Dna (136-mer) (42 kDa, DNA from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Protein ssx2 (2 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of SSX1 bound to the unmodified nucleosome at a resolution of 3.02 angstrom
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8hr1
Q-score: 0.532
Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L
Nat Struct Mol Biol (2024) 31 pp. 300-310 [ DOI: doi:10.1038/s41594-023-01141-1 Pubmed: 38177667 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ssx1 (1 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Ssx1-unmodified nucleosome complex (280 kDa, Complex from Homo sapiens)
cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7yqk
Q-score: 0.424
Ai H, Chu GC, Gong Q, Tong ZB, Deng Z, Liu X, Yang F, Xu Z, Li JB, Tian C, Liu L
J Am Chem Soc (2022) 144 pp. 18329-18337 [ DOI: doi:10.1021/jacs.2c06156 Pubmed: 36166692 ]
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Tp53-binding protein 1 (13 kDa, Protein from Homo sapiens)
- Histone h2ax (12 kDa, Protein from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b (10 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Udr motif of 53bp1 (2 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Complex of 53bp1(1484-1972) and gammah2axk15ub-h4k20me2 nucleosome (Complex from Homo sapiens)
cryo-EM structure of unmodified nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7xd1
Q-score: 0.558
Ai H, Sun M, Liu A, Sun Z, Liu T, Cao L, Liang L, Qu Q, Li Z, Deng Z, Tong Z, Chu G, Tian X, Deng H, Zhao S, Li JB, Lou Z, Liu L
Nat Chem Biol (2022) 18 pp. 972-980 [ Pubmed: 35739357 DOI: doi:10.1038/s41589-022-01067-7 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Unmodified nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)