Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 7ud5
Q-score: 0.263
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ Pubmed: 36095189 DOI: doi:10.1073/pnas.2205691119 ]
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Mll1 wrad complex (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Cdna flj56846, highly similar to zinc finger protein hrx (26 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Mll1 wrad complex bound to the ubiquitinated nucleosome (Complex)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
Resolution: 3.55 Å
EM Method: Single-particle
Fitted PDBs: 8du4
Q-score: 0.237
Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C
PNAS (2022) 119 pp. e2205691119-e2205691119 [ DOI: doi:10.1073/pnas.2205691119 Pubmed: 36095189 ]
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Rbbp5-wdr5 complex (Complex from Homo sapiens)
- Ubiquitinated nucleosome (Complex from Xenopus laevis)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
- Rbbp5-wdr5 complex bound to the ubiquitinated nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01
Ayoub A, Park SH, Lee YT, Cho US, Dou Y
Biochemistry (2022) 61 pp. 1-9 [ Pubmed: 34928138 DOI: doi:10.1021/acs.biochem.1c00603 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Rbbp5, wdr5, set1, and ash2l (Complex from Homo sapiens)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (mode01) (Complex)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode02
Ayoub A, Park SH, Lee YT, Cho US, Dou Y
Biochemistry (2022) 61 pp. 1-9 [ Pubmed: 34928138 DOI: doi:10.1021/acs.biochem.1c00603 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Rbbp5, wdr5, set1, and ash2l (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (mode02) (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
Resolution: 6.9 Å
EM Method: Single-particle
Fitted PDBs: 6w5i
Q-score: 0.135
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 6w5m
Q-score: 0.177
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 6w5n
Q-score: 0.167
Lee YT, Ayoub A, Park SH, Sha L, Xu J, Mao F, Zheng W, Zhang Y, Cho US, Dou Y
Nat Commun (2021) 12 pp. 2953-2953 [ DOI: doi:10.1038/s41467-021-23268-9 Pubmed: 34012049 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Dna (Complex from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5, wd repeat-containing protein 5, histone-lysine n-methyltransferase 2a, set1/ash2 histone methyltransferase complex subunit ash2 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 6pwv
Q-score: 0.188
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US
Nat Commun (2019) 10 pp. 5540-5540 [ Pubmed: 31804488 DOI: doi:10.1038/s41467-019-13550-2 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Human mll1 complex bound to the nucleosome (Complex from Xenopus laevis)
Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 6pww
Q-score: 0.26
Park SH, Ayoub A, Lee YT, Xu J, Kim H, Zheng W, Zhang B, Sha L, An S, Zhang Y, Cianfrocco MA, Su M, Dou Y, Cho US
Nat Commun (2019) 10 pp. 5540-5540 [ Pubmed: 31804488 DOI: doi:10.1038/s41467-019-13550-2 ]
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Rbbp5, wdr5, and mll1 in complex with the nucleosome (Complex from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6kiw
Q-score: 0.33
Xue H, Yao T, Cao M, Zhu G, Li Y, Yuan G, Chen Y, Lei M, Huang J
Nature (2019) 573 pp. 445-449 [ DOI: doi:10.1038/s41586-019-1528-1 Pubmed: 31485071 ]
- Human mll3 (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Human mll3 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase 2c (23 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)