Yeast COMPASS in complex with a ubiquitinated nucleosome
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 6ven
Q-score: 0.449
Worden EJ, Zhang X, Wolberger C
eLife (2020) 9 [ DOI: doi:10.7554/eLife.53199 Pubmed: 31922488 ]
- Histone-lysine n-methyltransferase, h3 lysine-4 specific (41 kDa, Protein from Saccharomyces cerevisiae)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- S-adenosylmethionine (398 Da, Ligand)
- Yeast compass (Complex from Saccharomyces cerevisiae)
- Ubiquitinated nucleosome (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Compass component sdc1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Compass component swd3 (34 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Compass component spp1 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Complex between yeast compass and a ubiquitinated nucleosome (Complex)
- Compass component swd1 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Compass component bre2 (58 kDa, Protein from Saccharomyces cerevisiae)
Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6nog
Q-score: 0.356
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ DOI: doi:10.1016/j.cell.2019.02.002 Pubmed: 30765112 ]
- Poised state dot1l in complex with the h2b-ub nucleosome (Complex)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2b-ub nucleosome (Complex)
- Histone core (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dot1l (Complex from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 1-to-1 complex
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 6nqa
Q-score: 0.436
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ DOI: doi:10.1016/j.cell.2019.02.002 Pubmed: 30765112 ]
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- H2b-ub nucleosome (Complex)
- Histone core (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dot1l (Complex from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Active state Dot1L bound to the H2B-Ubiquitinated nucleosome, 2-to-1 complex
Resolution: 2.96 Å
EM Method: Single-particle
Fitted PDBs: 6nj9
Q-score: 0.551
Worden EJ, Hoffmann NA, Hicks CW, Wolberger C
Cell (2019) 176 pp. 1490-1501.e12 [ DOI: doi:10.1016/j.cell.2019.02.002 Pubmed: 30765112 ]
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dot1l (Complex from Homo sapiens)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Histone core (Complex from Xenopus laevis)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (Complex from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- H2h2b-ub nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)