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 [ DOI: doi:10.1073/pnas.2205691119 Pubmed: 36095189 ]
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
- Mll1 wrad complex bound to the ubiquitinated nucleosome (Complex)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Mll1 wrad complex (Complex from Homo sapiens)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Cdna flj56846, highly similar to zinc finger protein hrx (26 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (9 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41467-019-13550-2 Pubmed: 31804488 ]
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Human mll1 complex bound to the nucleosome (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Protein dpy-30 homolog (11 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41467-019-13550-2 Pubmed: 31804488 ]
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Rbbp5, wdr5, and mll1 in complex with the nucleosome (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
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 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Human mll3 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 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)
- Human mll3 (Complex from Homo sapiens)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase 2c (23 kDa, Protein from Homo sapiens)
Cryo-EM structure of human MLL1-NCP complex, binding mode1
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6kix
Q-score: 0.338
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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Unmodified nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Human mll1 complex (Complex from Homo sapiens)
- Glutamine (146 Da, Ligand)
- Human mll1 complex associated with an unmodified nucleosome, binding mode 1 (Complex)
- Lysine (147 Da, Ligand)
Cryo-EM structure of human MLL1-NCP complex, binding mode2
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6kiz
Q-score: 0.31
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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Unmodified nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Human mll1 complex (Complex from Homo sapiens)
- Human mll1 complex associated with an unmodified nucleosome, binding mode 2 (Complex)
Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6kiu
Q-score: 0.461
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 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (3.2 angstrom) (Complex)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Human mll1 (Complex from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Glutamine (146 Da, Ligand)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Lysine (147 Da, Ligand)
Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6kiv
Q-score: 0.343
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 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Human mll1 complex (Complex from Homo sapiens)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)