Haspin bound to nucleosome in position 1
Resolution: 3.01 Å
EM Method: Single-particle
Fitted PDBs: 9b2s
Q-score: 0.536
Hicks CW, Gliech CR, Zhang X, Rahman S, Vasquez S, Holland AJ, Wolberger C
To Be Published
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Haspin bound to nucleosome (Complex from Xenopus laevis)
- Serine/threonine-protein kinase haspin (40 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Haspin bound to nucleosome in position 2
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 9b2t
Q-score: 0.502
Hicks CW, Gliech CR, Zhang X, Rahman S, Vasquez S, Holland AJ, Wolberger C
To Be Published
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Haspin bound to nucleosome (Complex from Xenopus laevis)
- Serine/threonine-protein kinase haspin (40 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (185-mer) (56 kDa, DNA from synthetic construct)
- 601 dna (185-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Resolution: 3.64 Å
EM Method: Single-particle
Fitted PDBs: 9b2u
Q-score: 0.363
Hicks CW, Gliech CR, Zhang X, Rahman S, Vasquez S, Holland AJ, Wolberger C
To Be Published
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Haspin bound to h3 tail (Complex from Xenopus laevis)
- Serine/threonine-protein kinase haspin (40 kDa, Protein from Homo sapiens)
Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8qzm
Q-score: 0.506
Wapenaar H, Clifford G, Rolls W, Pasquier M, Burdett H, Zhang Y, Deak G, Zou J, Spanos C, Taylor MRD, Mills J, Watson JA, Kumar D, Clark R, Das A, Valsakumar D, Bramham J, Voigt P, Sproul D, Wilson MD
EMBO Rep (2024) 25 pp. 5743-5779 [ Pubmed: 39528729 DOI: doi:10.1038/s44319-024-00306-3 ]
- Histone h3 (fragment) (15 kDa, Protein from Homo sapiens)
- Dna (145-mer) (59 kDa, DNA from synthetic construct)
- Ubiquitin (Complex from Homo sapiens)
- Dna (cytosine-5)-methyltransferase 3a (102 kDa, Protein from Homo sapiens)
- Dnmt3a1-dnmt3l complex (Complex from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- H2akc119ub nucleosome wrapped with 195 bp widom601 dna (Complex from Homo sapiens)
- Dnmt3a1-dnmt3l in complex with a human h2akc119ub nucleosome wrapped with 195bp of widom-601 positioning dna (147 kDa, Complex from Homo sapiens)
- Dna (145-mer) (60 kDa, DNA from synthetic construct)
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 ]
- E3 ubiquitin-protein ligase rnf168 (12 kDa, Protein from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (143-mer) (44 kDa, DNA 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)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 d3 (16 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (143-mer) (43 kDa, DNA from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
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 ]
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Human rybp-prc1 bound to h2ak118ub1 nucleosome (Complex from Homo sapiens)
- Ring1 and yy1-binding protein (25 kDa, Protein from Homo sapiens)
- Drosophila octamer (Complex from Drosophila melanogaster)
- Dna (Complex from Homo sapiens)
- Histone h2b (13 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Human rybp (Complex from Homo sapiens)
- Histone h2a (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Human ubiquitin (Complex from Homo sapiens)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Histone h3 (fragment) (15 kDa, Protein from Drosophila melanogaster)
- Ubiquitin-40s ribosomal protein s27a (fragment) (8 kDa, Protein from Homo sapiens)
human RYBP-PRC1 bound to mononucleosome
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8pp7
Q-score: 0.511
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 ]
- E3 ubiquitin-protein ligase ring2 (38 kDa, Protein from Homo sapiens)
- Drosophila octamer (Complex from Drosophila melanogaster)
- Dna (Complex from Homo sapiens)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Histone h2b (13 kDa, Protein from Drosophila melanogaster)
- Dna (215-mer) (76 kDa, DNA from Homo sapiens)
- Human rybp-prc1 bound to nucleosome (Complex from Homo sapiens)
- Polycomb complex protein bmi-1 (38 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Drosophila melanogaster)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Zinc ion (65 Da, Ligand)
- Histone h3 (fragment) (15 kDa, Protein from Drosophila melanogaster)
- Ring1b:bmi1 heterodimer (Complex from Homo sapiens)
Structure of Bre1-nucleosome complex - state1
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8t3y
Q-score: 0.503
Nat Struct Mol Biol (2023) 30 pp. 1623-1627 [ DOI: doi:10.1038/s41594-023-01137-x Pubmed: 37872231 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- E3 ubiquitin-protein ligase bre1 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Bre1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Cryo-EM structure of pioneer factor Cbf1 bound to the nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7ssa
Q-score: 0.449
Donovan BT, Chen H, Eek P, Meng Z, Jipa C, Tan S, Bai L, Poirier MG
Mol Cell (2023) 83 pp. 1251-1263.e6 [ DOI: doi:10.1016/j.molcel.2023.03.006 Pubmed: 36996811 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a.1 (13 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Centromere-binding protein 1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (137-mer) (46 kDa, DNA from synthetic construct)
- Centromere-binding protein 1 (39 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h3.2, histone h4 (Complex from Xenopus laevis)
- Dna (137-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a.1, histone h2b.1 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (Complex from synthetic construct)
- Pioneer factor cbf1 in complex with the nucleosome (286 kDa, Complex)