Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9jm0
Q-score: 0.492
Wang Y, Wang C, Guan Z, Cao J, Xu J, Wang S, Cui Y, Wang Q, Chen Y, Yin Y, Zhang D, Liu H, Sun M, Jin S, Tao P, Zou T
Cell Rep (2024) 43 pp. 114857-114857 [ DOI: doi:10.1016/j.celrep.2024.114857 Pubmed: 39395169 ]
- Retron ec86-effector fiber (Complex from Escherichia coli)
- [(2r,3s,4r,5r)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2r,3s,4r,5s)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate (559 Da, Ligand)
- Dna (85-mer) (26 kDa, DNA from Escherichia coli)
- Rna (82-mer) (26 kDa, RNA from Escherichia coli)
- Retron ec86 putative ribosyltransferase/dna-binding protein (35 kDa, Protein from Escherichia coli)
- Retron ec86 reverse transcriptase (37 kDa, Protein from Escherichia coli)
- Nicotinamide (122 Da, Ligand)
- Rna (5'-r(p*cp*gp*up*ap*ap*gp*gp*gp*up*gp*cp*gp*cp*a)-3') (4 kDa, RNA from Escherichia coli)
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 ]
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA 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)
- Rnf168/ubch5c-ub/nucleosomes determined by intein-based e2-ub-ncp conjugation strategy (Complex from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 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 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)
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- 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)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
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 h4 (9 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (12 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)
- 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)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
Structure of the asymmetric unit of SFTSV virion
Resolution: 5.2 Å
EM Method: Single-particle
Fitted PDBs: 8i4t
Q-score: 0.206
Du S, Peng R, Xu W, Qu X, Wang Y, Wang J, Li L, Tian M, Guan Y, Wang J, Wang G, Li H, Deng L, Shi X, Ma Y, Liu F, Sun M, Wei Z, Jin N, Liu W, Qi J, Liu Q, Liao M, Li C
Nat Commun (2023) 14 pp. 6333-6333 [ Pubmed: 37816705 DOI: doi:10.1038/s41467-023-41804-7 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dabie bandavirus (Virus from Dabie bandavirus)
- Envelopment polyprotein (61 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
- Envelopment polyprotein (54 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
Structure of SFTSV Gn-Gc heterodimer
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8ilq
Q-score: 0.419
Du S, Peng R, Xu W, Qu X, Wang Y, Wang J, Li L, Tian M, Guan Y, Wang J, Wang G, Li H, Deng L, Shi X, Ma Y, Liu F, Sun M, Wei Z, Jin N, Liu W, Qi J, Liu Q, Liao M, Li C
Nat Commun (2023) 14 pp. 6333-6333 [ Pubmed: 37816705 DOI: doi:10.1038/s41467-023-41804-7 ]
- Dabie bandavirus (Virus from Dabie bandavirus)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Envelopment polyprotein (61 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
- Envelopment polyprotein (54 kDa, Protein from Severe fever with thrombocytopenia syndrome virus)
Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8ieg
Q-score: 0.393
Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L
Mol Cell (2023) 83 pp. 3080-3094.e14 [ DOI: doi:10.1016/j.molcel.2023.08.001 Pubmed: 37633270 ]
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- E3 ubiquitin-protein ligase bre1 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 2 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Bre1(mrbd-ring)/rad6-ub in complex with nucleosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
RNF20-RNF40/hRad6A-Ub/nucleosome complex
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8iej
Q-score: 0.461
Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L
Mol Cell (2023) 83 pp. 3080-3094.e14 [ DOI: doi:10.1016/j.molcel.2023.08.001 Pubmed: 37633270 ]
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase bre1a (7 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 a (17 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Rnf20-rnf40/hrad6a-ub in complex with nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase bre1b (7 kDa, Protein 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 h3 (11 kDa, Protein from Homo sapiens)
- Ubch5b (16 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from Homo sapiens)
- Ring1b (11 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Commd3 protein (11 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Complex of prc1 and h2ak119-ubch5b-ub nucleosome (350 kDa, Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (9 kDa, Protein 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 ]
- Ubiquitin-conjugating enzyme e2d 3 (ubc4/5 homolog, yeast), isoform cra_a (16 kDa, Protein from Homo sapiens)
- Histone h2a type 1-h (12 kDa, Protein from Homo sapiens)
- Histone h3 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- H2b (20 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)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Brca1-associated ring domain protein 1 (10 kDa, Protein from Homo sapiens)
- Complex of brca1/bard1 and h2ak127-ubch5c-ub nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)