cryo-EM structure of human H2A.B nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 6m4g
Q-score: 0.493
Zhou M, Dai L, Li C, Shi L, Huang Y, Guo Z, Wu F, Zhu P, Zhou Z
EMBO J (2021) 40 pp. e105907-e105907 [ Pubmed: 33073403 DOI: doi:10.15252/embj.2020105907 ]
- Dna (93-mer) (45 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- H2a.b nucleosome (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a-bbd type 2/3 (12 kDa, Protein from Homo sapiens)
- Dna (93-mer) (45 kDa, DNA from Homo sapiens)
Structure of human Sox11 transcription factor in complex with a nucleosome
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6t7a
Q-score: 0.37
Dodonova SO, Zhu F, Dienemann C, Taipale J, Cramer P
Nature (2020) 580 pp. 669-672 [ DOI: doi:10.1038/s41586-020-2195-y Pubmed: 32350470 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Structure of human sox11 transcription factor in complex with a nucleosome (218 kDa, Complex)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Sox11 transcription factor, histones (Complex from Homo sapiens)
- Transcription factor sox-11 (12 kDa, Protein from Homo sapiens)
SAGA-TBP filtered to show the position of the DUB domain
Resolution: 20.0 Å
EM Method: Single-particle
Fitted PDBs: 6tbm
Q-score: 0.08
Papai G, Frechard A, Kolesnikova O, Crucifix C, Schultz P, Ben-Shem A
Nature (2020) 577 pp. 711-716 [ DOI: doi:10.1038/s41586-020-1944-2 Pubmed: 31969704 ]
- Tata-box binding protein (tbp) (Complex from Komagataella phaffii GS115)
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Tata-box binding protein (tbp) (27 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription and mrna export factor sus1 (11 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription initiation factor tfiid subunit 10 (23 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Saga component (Complex from Komagataella phaffii GS115)
- Saga complex (Complex from Komagataella phaffii GS115)
- Transcriptional regulator involved in glucose repression of gal4p-regulated genes (81 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Ubiquitin carboxyl-terminal hydrolase (56 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of the saga and saga-like transcriptional regulatory complexes, interacts with spt15p to act (39 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of the saga transcriptional regulatory complex, involved in proper assembly of the complex (136 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt8 (34 kDa, Protein from Komagataella phaffii GS115)
- Spt20 (59 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (60 kda) of tfiid and saga complexes (54 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (90 kda) of tfiid and saga complexes (80 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcriptional coactivator hfi1/ada1 (49 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (61/68 kda) of tfiid and saga complexes (66 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Polyubiquitin-b (Complex from Homo sapiens)
- Water (18 Da, Ligand)
- Saga bound to tbp (1 MDa, Complex)
- Saga-associated factor 11 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit of saga histone acetyltransferase complex (79 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription-associated protein (438 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Subunit (17 kda) of tfiid and saga complexes, involved in rna polymerase ii transcription initiation (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
Structure of a Yeast Centromeric Nucleosome at 2.7 Angstrom resolution
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6uph
Q-score: 0.623
Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC, Ciferri C, Dimitrova YN
Structure (2020) 28 pp. 363-370.e3 [ DOI: doi:10.1016/j.str.2019.12.002 Pubmed: 32004465 ]
- Dna (119-mer) (45 kDa, DNA from unidentified)
- Histone h2b.1 (16 kDa, Protein from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
- Histone h2a (15 kDa, Protein from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
- Histone h3-like centromeric protein cse4 (26 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4, histone h2a, histone h2b.1 (Complex from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
- Dna (119-mer) (45 kDa, DNA from unidentified)
- Yeast centromeric nucleosome (240 MDa, Complex)
- Dna (Complex from unidentified)
- Histone h3-like centromeric protein cse4 (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6muo
Q-score: 0.369
Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE
Curr Biol (2019) 29 pp. 2625-2639.e5 [ Pubmed: 31353180 DOI: doi:10.1016/j.cub.2019.06.062 ]
- Cenp-a chromatin complex bound with cenp-c and cenp-n of ccan kinetochore components (276 kDa, Cellular component from Homo sapiens)
- Histone h2b type 2-f (10 kDa, Protein from Homo sapiens)
- Histone h4 (10 kDa, Protein from Homo sapiens)
- Dna/rna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3-like centromeric protein a (11 kDa, Protein from Homo sapiens)
- Centromere protein c (2 kDa, Protein from Homo sapiens)
- Centromere protein n (25 kDa, Protein from Homo sapiens)
- Dna/rna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-c (11 kDa, Protein from Homo sapiens)
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 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone core (Complex from Xenopus laevis)
- Ubiquitin (Complex from Homo sapiens)
- H2b-ub nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Dot1l (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Poised state dot1l in complex with the h2b-ub nucleosome (Complex)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6c0w
Q-score: 0.39
Pentakota S, Zhou K, Smith C, Maffini S, Petrovic A, Morgan GP, Weir JR, Vetter IR, Musacchio A, Luger K
eLife (2017) 6 [ DOI: doi:10.7554/eLife.33442 Pubmed: 29280735 ]
- Complex of cenp-a nucleosome with cenp-n (230 kDa, Complex from Homo sapiens)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- 147 mer dna (45 kDa, DNA from Escherichia coli)
- Histone h3-like centromeric protein a (16 kDa, Protein from Homo sapiens)
- 147 mer dna (45 kDa, DNA from Escherichia coli)
- Centromere protein n (34 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)