Cryo-EM structure of the centromeric nucleosome with native alpha satellite DNA
Resolution: 3.395 Å
EM Method: Single-particle
Fitted PDBs: 6o1d
Q-score: 0.482
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P
Nat Commun (2019) 10 pp. 2301-2301 [ Pubmed: 31127102 DOI: doi:10.1038/s41467-019-10247-4 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Cenp-a nucleosome with native alpha satellite dna sequence (Complex from Homo sapiens)
- Histone h3-like centromeric protein a (18 kDa, Protein from Homo sapiens)
Cryo-EM structure of the CENP-A nucleosome (W601) in complex with a single chain antibody fragment
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 6e0c
Q-score: 0.59
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P
Nat Commun (2019) 10 pp. 2301-2301 [ Pubmed: 31127102 DOI: doi:10.1038/s41467-019-10247-4 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli)
- Scfv (29 kDa, Protein from Mus musculus)
- Cenp-a nucleosome (w601) complex (Complex from Homo sapiens)
- Histone h3-like centromeric protein a (18 kDa, Protein from Homo sapiens)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 6e0p
Q-score: 0.57
Zhou BR, Yadav KNS, Borgnia M, Hong J, Cao B, Olins AL, Olins DE, Bai Y, Zhang P
Nat Commun (2019) 10 pp. 2301-2301 [ Pubmed: 31127102 DOI: doi:10.1038/s41467-019-10247-4 ]
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cenp-a nucleosome and antibody complex (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Scfv (29 kDa, Protein from Mus musculus)
- Dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h3-like centromeric protein a (18 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 h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Ubiquitin (Complex from Homo sapiens)
- Poised state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- H2b-ub nucleosome (Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Dot1l (Complex from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone core (Complex 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 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Dot1l (Complex from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- H2b-ub nucleosome (Complex)
- Histone h2a type 1 (13 kDa, Protein 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 h3.2 (15 kDa, Protein from Xenopus laevis)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone core (Complex 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 [ Pubmed: 30765112 DOI: doi:10.1016/j.cell.2019.02.002 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Active state dot1l in complex with the h2b-ub nucleosome (Complex)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (Complex from Homo sapiens)
- H2h2b-ub nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Dot1l (Complex from Homo sapiens)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
- Histone core (Complex from Xenopus laevis)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 6ir9
Q-score: 0.264
Ehara H, Kujirai T, Fujino Y, Shirouzu M, Kurumizaka H, Sekine SI
Science (2019) 363 pp. 744-747 [ Pubmed: 30733384 DOI: doi:10.1126/science.aav8912 ]
- Rna polymerase subunit abc10-beta, common to rna polymerases i, ii, and iii (8 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Spt5 (101 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase subunit abc10-alpha (7 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Dna (198-mer) (60 kDa, DNA from synthetic construct)
- Rna polymerase subunit abc27, common to rna polymerases i, ii, and iii (24 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Rna polymerase ii subunit (18 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor spt4 (12 kDa, Protein from Komagataella phaffii)
- Rna polymerase ii elongation complex bound with elf1 and spt4/5, stalled at shl(-1) of the nucleosome (Complex from Komagataella phaffii)
- Rna (5'-r(p*gp*cp*cp*up*gp*gp*up*gp*up*cp*up*up*gp*gp*gp*u)-3') (5 kDa, RNA from synthetic construct)
- Rna polymerase ii third largest subunit b44, part of central core (34 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit beta (139 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (194 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h3.3 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Rna polymerase subunit abc23, common to rna polymerases i, ii, and iii (17 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Transcription elongation factor 1 homolog (12 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerase subunit (13 kDa, Protein from Komagataella phaffii (strain ATCC 76273 / CBS 7435 / CECT 11047 / NRRL Y-11430 / Wegner 21-1))
- Magnesium ion (24 Da, Ligand)
- Rna polymerase ii subunit b12.5 (13 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna polymerase ii subunit b32 (20 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (16 kDa, Protein from Komagataella phaffii (strain GS115 / ATCC 20864))
- Dna (198-mer) (61 kDa, DNA from synthetic construct)
Structure of Dot1L-H2BK120ub nucleosome complex
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6nn6
Q-score: 0.371
Anderson CJ, Baird MR, Hsu A, Barbour EH, Koyama Y, Borgnia MJ, McGinty RK
Cell Rep (2019) 26 pp. 1681-1690.e5 [ DOI: doi:10.1016/j.celrep.2019.01.058 Pubmed: 30759380 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dot1l-h2bk120ub nucleosome complex (class 2a) (270 kDa, Complex from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
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 [ Pubmed: 29280735 DOI: doi:10.7554/eLife.33442 ]
- 147 mer dna (45 kDa, DNA from Escherichia coli)
- Complex of cenp-a nucleosome with cenp-n (230 kDa, Complex from Homo sapiens)
- 147 mer dna (45 kDa, DNA from Escherichia coli)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Centromere protein n (34 kDa, Protein from Homo sapiens)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Histone h3-like centromeric protein a (16 kDa, Protein from Homo sapiens)
Cryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N
Resolution: 3.92 Å
EM Method: Single-particle
Fitted PDBs: 6buz
Q-score: 0.372
Chittori S, Hong J, Saunders H, Feng H, Ghirlando R, Kelly AE, Bai Y, Subramaniam S
Science (2018) 359 pp. 339-343 [ Pubmed: 29269420 DOI: doi:10.1126/science.aar2781 ]
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3-like centromeric protein a (18 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b (13 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Homo sapiens)
- Centromeric nucleosome in complex with kinetochore protein cenp-n (Complex from Homo sapiens)
- Maltose-binding periplasmic protein, centromere protein n chimera (75 kDa, Protein from Homo sapiens)