Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrg
Q-score: 0.227
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone (Complex from Homo sapiens)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Histone methyltransferase and nucleosome complex (Complex)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
- Histone,suv420h1 (Complex from Xenopus laevis)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction)
Resolution: 4.42 Å
EM Method: Single-particle
Fitted PDBs: 7kbf
Q-score: 0.29
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Dna (184-mer) (53 kDa, DNA from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (184-mer) (53 kDa, DNA from Xenopus laevis)
- Protein b4 (29 kDa, Protein from Xenopus laevis)
- H1.8 bound nucleosome isolated from metaphase chromosome in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 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 ]
- Histone h3.2, histone h4, histone h2a type 1, histone h2b 1.1 (Complex from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Dna (147-mer) (45 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- 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)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Mll1 in complex with rbbp5, wdr5, set1, and ash2l bound to the nucleosome (380 kDa, Complex)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 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 ]
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wd repeat-containing protein 5 (34 kDa, Protein from Homo sapiens)
- Rbbp5, wdr5, and mll1 in complex with the nucleosome (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
Cryo-EM structure of RbBP5 bound to the nucleosome
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 6pwx
Q-score: 0.332
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 ]
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Rbbp5 in complex with the nucleosome (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 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 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase 2c (23 kDa, Protein from Homo sapiens)
- Human mll3 (Complex from Homo sapiens)
- Human mll3 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 ]
- Human mll1 complex associated with an unmodified nucleosome, binding mode 1 (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Lysine (147 Da, Ligand)
- Unmodified nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Glutamine (146 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Human mll1 complex (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Human mll1 complex associated with an unmodified nucleosome, binding mode 2 (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Unmodified nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Human mll1 complex (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 ]
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Human mll1 complex (Complex from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state
Resolution: 4.31 Å
EM Method: Single-particle
Fitted PDBs: 5z3u
Q-score: 0.372
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ DOI: doi:10.1038/s41586-019-1029-2 Pubmed: 30867599 ]
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Complex of snf2 and nucleosome in adp befx state (300 kDa, Complex from Xenopus laevis)