Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C
Sci Adv (2024) 10 pp. eadp0975-eadp0975 [ DOI: doi:10.1126/sciadv.adp0975 Pubmed: 39196936 ]
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dnmt3a1 udr in complex with h2ak119ub-nucleosome (Complex from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (cytosine-5)-methyltransferase 3a (9 kDa, Protein from Homo sapiens)
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8t9h
Q-score: 0.393
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell (2023) 83 pp. 2872-2883.e7 [ DOI: doi:10.1016/j.molcel.2023.07.020 Pubmed: 37595555 ]
- Dna (146-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone-lysine n-methyltransferase kmt5b (44 kDa, Protein from Homo sapiens)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Suv420h1-h2a.z nucleosome complex (Complex from Xenopus laevis)
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8t9f
Q-score: 0.516
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell (2023) 83 pp. 2872-2883.e7 [ DOI: doi:10.1016/j.molcel.2023.07.020 Pubmed: 37595555 ]
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Dna (122-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase kmt5b (44 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (122-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Suv420h1-h2a.z nucleosome complex (Complex from Xenopus laevis)
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell (2023) 83 pp. 2872-2883.e7 [ DOI: doi:10.1016/j.molcel.2023.07.020 Pubmed: 37595555 ]
- Histone-lysine n-methyltransferase kmt5b peptide (2 kDa, Protein from Homo sapiens)
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (132-mer) (44 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Dna (132-mer) (45 kDa, DNA from Escherichia coli 'BL21-Gold(DE3)pLysS AG')
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Suv420h1-h2a.z nucleosome complex (Complex from Xenopus laevis)
Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8thu
Q-score: 0.508
Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ
Mol Cell (2023) 83 pp. 2872-2883.e7 [ DOI: doi:10.1016/j.molcel.2023.07.020 Pubmed: 37595555 ]
- Histone h2a.z (13 kDa, Protein from Homo sapiens)
- Dna (145-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (146-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)
- Suv420h1-h2a.z nucleosome complex (Complex from Xenopus laevis)
BAP1/ASXL1 bound to the H2AK119Ub Nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8svf
Q-score: 0.383
Thomas JF, Valencia-Sanchez MI, Tamburri S, Gloor SL, Rustichelli S, Godinez-Lopez V, De Ioannes P, Lee R, Abini-Agbomson S, Gretarsson K, Burg JM, Hickman AR, Sun L, Gopinath S, Taylor HF, Sun ZW, Ezell RJ, Vaidya A, Meiners MJ, Cheek MA, Rice WJ, Svetlov V, Nudler E, Lu C, Keogh MC, Pasini D, Armache KJ
Sci Adv (2023) 9 pp. eadg9832-eadg9832 [ DOI: doi:10.1126/sciadv.adg9832 Pubmed: 37556531 ]
- Ubiquitin carboxyl-terminal hydrolase bap1 (80 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna/rna (187-mer) (58 kDa, Macromolecule from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna/rna (327-mer) (102 kDa, Macromolecule from synthetic construct)
- Bap1/asxl1 bound to the h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Polycomb group protein asxl1 (165 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Active state Dot1 bound to the unacetylated H4 nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7k6p
Q-score: 0.473
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Dna (146-mer) (Complex from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (46 kDa, Protein from Saccharomyces cerevisiae)
- S-adenosylmethionine (398 Da, Ligand)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (11 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histone h3.2 (11 kDa, Protein from Xenopus laevis)
- Histone h4 (10 kDa, Protein from Xenopus laevis)
- Active state dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Polyubiquitin-b (Complex from Homo sapiens)
Active state Dot1 bound to the H4K16ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7k6q
Q-score: 0.489
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (46 kDa, Protein from Saccharomyces cerevisiae)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Dna (146-mer) (44 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (11 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histone h3.2 (11 kDa, Protein from Xenopus laevis)
- Histone h4 (10 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Dna (146-mer) (Complex from Synthetic construct)
- Active state dot1 bound to the h4k16ac nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Polyubiquitin-b (Complex from Homo sapiens)
Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Histone h3.2 (Protein from Xenopus lenduensis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Polyubiquitin-b (Protein from Homo sapiens)
- Noncatalytic conformation dot1 bound to the unacetylated h4 nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Saccharomyces cerevisiae)
- Dna (146-mer) (Complex from Synthetic)
- Polyubiquitin-b (Complex from Homo sap)
Active state Dot1 bound to the H4K16ac nucleosome, Ubiquitin focused map
Valencia-Sanchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ
Science (2021) 371 [ DOI: doi:10.1126/science.abc6663 Pubmed: 33479126 ]
- Active state dot1 bound to the h4k16 acetylated nucleosome (Complex from Saccharomyces cerevisiae)
- Polyubiquitin-b (Protein from Xenopus laevis)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- Dna (146-mer) (DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase, h3 lysine-79 specific (Complex from Saccharomyces cerevisiae)
- Dna (146-mer) (Complex from Synthetic)
- Polyubiquitin-b (Complex from Homo sap)