Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd3
Q-score: 0.376
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8kd4
Q-score: 0.373
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd5
Q-score: 0.378
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (Complex from synthetic construct)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp (187bp/mla) class2 (Complex)
- Histone (Complex from Xenopus laevis)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kd6
Q-score: 0.311
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- Dna (Complex)
Yeast Set2 bound to a nucleosome containing oncohistone mutations
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7ea5
Q-score: 0.473
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J
Cell Discov (2021) 7 pp. 32-32 [ DOI: doi:10.1038/s41421-021-00261-6 Pubmed: 33972509 ]
- Histone-lysine n-methyltransferase, h3 lysine-36 specific (26 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- 601-dna (44 kDa, DNA from synthetic construct)
- 601-dna (44 kDa, DNA from synthetic construct)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Histone h3 (11 kDa, Protein from Xenopus laevis)
- Histone h4 (8 kDa, Protein from Xenopus laevis)
- The set2-nucleosome(h3k36m)complex structure (Complex from Xenopus laevis)
Human SETD2 bound to a nucleosome containing oncohistone mutations
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7ea8
Q-score: 0.509
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J
Cell Discov (2021) 7 pp. 32-32 [ DOI: doi:10.1038/s41421-021-00261-6 Pubmed: 33972509 ]
- Histone h2a type 1-d (11 kDa, Protein from Homo sapiens)
- Histone h4 (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (Complex from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h3.3 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- 601-dna (37 kDa, DNA from synthetic construct)
- Histone (Complex)
- 601-dna (37 kDa, DNA from synthetic construct)
- Dna (Complex)
- Human setd2-ncp(h3.3k36m)-sam complex structure (Complex from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (28 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 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 (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 ]
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (3.2 angstrom) (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Lysine (147 Da, Ligand)
- Human mll1 (Complex from Homo sapiens)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Glutamine (146 Da, Ligand)
- 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)
- 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)