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 [ Pubmed: 33972509 DOI: doi:10.1038/s41421-021-00261-6 ]
- Histone h4 (8 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- The set2-nucleosome(h3k36m)complex structure (Complex from Xenopus laevis)
- 601-dna (44 kDa, DNA from synthetic construct)
- Histone h2b (10 kDa, Protein from Xenopus laevis)
- Histone h2a (11 kDa, Protein from Xenopus laevis)
- Histone h3 (11 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 601-dna (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-36 specific (26 kDa, Protein from Saccharomyces cerevisiae)
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-lysine n-methyltransferase setd2 (28 kDa, Protein from Homo sapiens)
- Histone h4 (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase setd2 (Complex from Homo sapiens)
- Human setd2-ncp(h3.3k36m)-sam complex structure (Complex from Homo sapiens)
- Histone h2b type 2-e (13 kDa, Protein from Homo sapiens)
- 601-dna (37 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- S-adenosylmethionine (398 Da, Ligand)
- Histone (Complex)
- 601-dna (37 kDa, DNA from synthetic construct)
- Histone h3.3 (11 kDa, Protein from Homo sapiens)
- Dna (Complex)
- Histone h2a type 1-d (11 kDa, Protein from Homo sapiens)
cryo-EM structure of human RNA polymerase III in elongating state
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 7d58
Q-score: 0.014
Wang Q, Li S, Wan F, Xu Y, Wu Z, Cao M, Lan P, Lei M, Wu J
Nat Struct Mol Biol (2021) 28 pp. 220-227 [ Pubmed: 33558766 DOI: doi:10.1038/s41594-021-00557-x ]
- Dna-directed rna polymerase iii subunit rpc6 (35 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc1 (24 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac1 (39 kDa, Protein from Homo sapiens)
- Non-template dna (12 kDa, DNA from Homo sapiens)
- Human pol3 ec (Complex from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc7 (25 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc1 (155 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc8 (22 kDa, Protein from Homo sapiens)
- Template dna (12 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc9 (16 kDa, Protein from Homo sapiens)
- Rna (6 kDa, RNA from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc5 (80 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc3 (60 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc4 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc4 (7 kDa, Protein from Homo sapiens)
- Iron/sulfur cluster (351 Da, Ligand)
- Dna-directed rna polymerase iii subunit rpc10 (12 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc2 (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i and iii subunit rpac2 (15 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase iii subunit rpc2 (127 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 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Human mll3 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- 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)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Glutamine (146 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Human mll1 complex (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Human mll1 complex associated with an unmodified nucleosome, binding mode 1 (Complex)
- Lysine (147 Da, Ligand)
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Unmodified nucleosome (Complex 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 [ Pubmed: 31485071 DOI: doi:10.1038/s41586-019-1528-1 ]
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Unmodified nucleosome (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Human mll1 complex associated with an unmodified nucleosome, binding mode 2 (Complex)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Human mll1 complex (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
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 [ Pubmed: 31485071 DOI: doi:10.1038/s41586-019-1528-1 ]
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (3.2 angstrom) (Complex)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Glutamine (146 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Human mll1 (Complex from Homo sapiens)
- Histone h2b 1.1 (13 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)
- 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 [ Pubmed: 31485071 DOI: doi:10.1038/s41586-019-1528-1 ]
- Wd repeat-containing protein 5 (36 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H2b-monoubiquitinated nucleosome (Complex from Xenopus laevis)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase 2a (24 kDa, Protein from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Retinoblastoma-binding protein 5 (59 kDa, Protein from Homo sapiens)
- Human mll1 complex associated with an h2b-monoubiquitinated nucleosome (4.0 angstrom) (Complex)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Set1/ash2 histone methyltransferase complex subunit ash2 (60 kDa, Protein from Homo sapiens)
- Human mll1 complex (Complex from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6j99
Q-score: 0.132
Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J
Cell Res (2019) 29 pp. 330-333 [ DOI: doi:10.1038/s41422-019-0146-7 Pubmed: 30770869 ]
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (145-mer) (45 kDa, DNA from synthetic construct)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- S-adenosyl-l-homocysteine (384 Da, Ligand)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (47 kDa, Protein from Homo sapiens)
- Dna (144-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (Complex from Human)
- Human dot1l in complex with an h2b-monoubiquitinated nucleosome (250 kDa, Complex from African clawed frog)