Chromosome Passenger Complex (CPC) localization module in complex with H3.T3p-nucleosome
Resolution: 2.42 Å
EM Method: Single-particle
Fitted PDBs: 8rup
Q-score: 0.551
Ruza RR, Chung CW, Gold DB, Serena M, Roberts E, Gruneberg U, Barr FA
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.22.634029 ]
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (47 kDa, DNA from synthetic construct)
- Inner centromere protein (9 kDa, Protein from Homo sapiens)
- Chromosome passenger complex localisation module (Complex from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Baculoviral iap repeat-containing protein 5 (16 kDa, Protein from Homo sapiens)
- Dna (147-mer) (46 kDa, DNA from synthetic construct)
- H3.t3p-nucleosome (Complex from Xenopus laevis)
- Borealin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Human cpc localisation module in complex with xenopus h3.t3p-nucleosome (202 kDa, Complex from Homo sapiens)
Structure of human APC3loop 375-381 bound to the NCP
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9fgq
Q-score: 0.651
Cirillo L, Young R, Veerapathiran S, Roberti A, Martin M, Abubacar A, Perosa C, Coates C, Muhammad R, Roumeliotis TI, Choudhary JS, Alfieri C, Pines J
EMBO J (2024) 43 pp. 4324-4355 [ DOI: doi:10.1038/s44318-024-00194-2 Pubmed: 39143240 ]
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Dna (132-mer) (64 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (131-mer) (65 kDa, DNA from Homo sapiens)
- Histone h2b type 1-b (29 kDa, Protein from Homo sapiens)
- Cell division cycle protein 27 homolog (32 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Apc3 motif bound to the ncp acidic patch (Complex from Homo sapiens)
Structure of DDM1-nucleosome complex in ADP state
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8wh8
Q-score: 0.403
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Ddm1-nucleosome complex in adp state (290 kDa, Complex from Arabidopsis thaliana)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in ADP-BeFx state
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 8wh9
Q-score: 0.336
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Ddm1-nucleosome complex in adp-befx state (290 kDa, Complex from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2
Resolution: 4.05 Å
EM Method: Single-particle
Fitted PDBs: 8wha
Q-score: 0.306
Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J
Nat Plants (2024) 10 pp. 374-380 [ Pubmed: 38413824 DOI: doi:10.1038/s41477-024-01640-z ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.1 (15 kDa, Protein from Arabidopsis thaliana)
- Dna (sense strand) (45 kDa, DNA from synthetic construct)
- Atp-dependent dna helicase ddm1 (86 kDa, Protein from Arabidopsis thaliana)
- Histone h2b.6 (16 kDa, Protein from Arabidopsis thaliana)
- Dna (antisense strand) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Arabidopsis thaliana)
- Beryllium trifluoride ion (66 Da, Ligand)
- Ddm1-nucleosome complex in the adp-befx state with ddm1 bound to shl2 and shl-2 (376 kDa, Complex from Arabidopsis thaliana)
- Histone h2a.6 (13 kDa, Protein from Arabidopsis thaliana)
human RYBP-PRC1 bound to H2AK118ub1 nucleosome
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8pp6
Q-score: 0.465
Ciapponi M, Karlukova E, Schkolziger S, Benda C, Muller J
Nat Struct Mol Biol (2024) 31 pp. 1023-1027 [ DOI: doi:10.1038/s41594-024-01258-x Pubmed: 38528151 ]
- Histone h3 (fragment) (15 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Drosophila octamer (Complex from Drosophila melanogaster)
- Ring1 and yy1-binding protein (25 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Drosophila melanogaster)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (fragment) (8 kDa, Protein from Homo sapiens)
- Human rybp (Complex from Homo sapiens)
- Human rybp-prc1 bound to h2ak118ub1 nucleosome (Complex from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Human ubiquitin (Complex from Homo sapiens)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8sn3
Q-score: 0.429
Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G
Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn4
Q-score: 0.439
Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G
Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8sn5
Q-score: 0.41
Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G
Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 8sn6
Q-score: 0.434
Hu Q, Zhao D, Cui G, Bhandari J, Thompson JR, Botuyan MV, Mer G
Mol Cell (2024) 84 pp. 839-853.e12 [ Pubmed: 38242129 DOI: doi:10.1016/j.molcel.2023.12.036 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 d3 (17 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase rnf168 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (13 kDa, Protein from Homo sapiens)
- Human nucleosome core particle in complex with rnf168 and ubch5c~ub (256 kDa, Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)