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 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 PRC1 bound to H2AK119-UbcH5b-Ub nucleosome
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8grm
Q-score: 0.516
Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L
Chem (2023) [ DOI: doi:10.1016/j.chempr.2023.01.012 ]
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Ubch5b (16 kDa, Protein from Homo sapiens)
- Commd3 protein (11 kDa, Protein from Homo sapiens)
- Ring1b (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)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Complex of prc1 and h2ak119-ubch5b-ub nucleosome (350 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
Cryo-EM structure of BRCA1/BARD1 bound to H2AK127-UbcH5c-Ub nucleosome
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 8grq
Q-score: 0.352
Ai HS, Tong Z, Deng Z, Tian J, Zhang L, Sun M, Du Y, Xu Z, Shi Q, Liang L, Zheng Q, Li JB, Pan M, Liu L
Chem (2023) [ DOI: doi:10.1016/j.chempr.2023.01.012 ]
- Histone h2a type 1-h (12 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Breast cancer type 1 susceptibility protein (10 kDa, Protein from Homo sapiens)
- Complex of brca1/bard1 and h2ak127-ubch5c-ub nucleosome (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Brca1-associated ring domain protein 1 (10 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2d 3 (ubc4/5 homolog, yeast), isoform cra_a (16 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- H2b (20 kDa, Protein from Homo sapiens)
Structure of yeast Ubr1 in complex with Ubc2 and N-degron
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7mex
Q-score: 0.45
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ DOI: doi:10.1038/s41586-021-04097-8 Pubmed: 34789879 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- N-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast ubr1 in complex with ubc2 and n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 7mey
Q-score: 0.407
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ Pubmed: 34789879 DOI: doi:10.1038/s41586-021-04097-8 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Monoubiquitinated n-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast ubr1 in complex with ubc2 and monoubiquitinated n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 2-(ethylamino)ethane-1-thiol (105 Da, Ligand)