SIRT6 bound to an H3K9Ac nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f86
Q-score: 0.434
Wang ZA, Markert JW, Whedon SD, Yapa Abeywardana M, Lee K, Jiang H, Suarez C, Lin H, Farnung L, Cole PA
J Am Chem Soc (2023) 145 pp. 6811-6822 [ Pubmed: 36930461 DOI: doi:10.1021/jacs.2c13512 ]
- Sirt6 bound to h3k9ac (Complex)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl [(3ar,5r,6r,6ar)-6-hydroxytetrahydro-2h-furo[2,3-d][1,3]oxathiol-5-yl]methyl dihydrogen diphosphate (non-preferred name) (587 Da, Ligand)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
NSD2 bearing E1099K/T1150A dual mutation in complex with 187-bp NCP
Resolution: 3.75 Å
EM Method: Single-particle
Fitted PDBs: 7cro
Q-score: 0.448
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd2 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd2 (79 kDa, Protein from Homo sapiens)
- Histone h3, h4, h2a and h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nsd2 bearing e1099k/t1150a dual mutation in complex with 187-bp ncp (300 kDa, Complex)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7crp
Q-score: 0.542
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd3 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Nsd3 bearing e1181k/t1232a dual mutation in complex with 187-bp ncp (1:1 binding mode) (300 kDa, Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 7crq
Q-score: 0.507
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Nsd3 (Complex from Homo sapiens)
- Dna (Complex from Xenopus laevis)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)
- Nsd3 bearing e1181k/t1232a dual mutation in complex with 187-bp ncp (2:1 binding mode) (300 kDa, Complex)
Native NSD3 bound to 187-bp nucleosome
Resolution: 3.48 Å
EM Method: Single-particle
Fitted PDBs: 7crr
Q-score: 0.464
Li W, Tian W, Yuan G, Deng P, Sengupta D, Cheng Z, Cao Y, Ren J, Qin Y, Zhou Y, Jia Y, Gozani O, Patel DJ, Wang Z
Nature (2021) 590 pp. 498-503 [ DOI: doi:10.1038/s41586-020-03069-8 Pubmed: 33361816 ]
- Cryo-em structure of the native nsd3 bound to 187-bp nucleosome (300 kDa, Complex)
- Histone h3, h4, h2a, h2b (Complex from Xenopus laevis)
- Histone-lysine n-methyltransferase nsd3 (85 kDa, Protein from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Dna(168-mer) (57 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Native nsd3 (Complex from Homo sapiens)
- Dna (168-mer) (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h2b (13 kDa, Protein from Xenopus tropicalis)