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)
The 4x177 nucleosome array containing H1
Resolution: 9.5 Å
EM Method: Single-particle
Fitted PDBs: 7pet
Q-score: 0.105
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Tetranucleosome from 4x177 nucleosome array (Complex)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (702-mer) (218 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (702-mer) (215 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Trinucleosome of the 4x177 nucleosome array containing H1
Resolution: 7.2 Å
EM Method: Single-particle
Fitted PDBs: 7peu
Q-score: 0.138
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (522-mer) (160 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (522-mer) (161 kDa, DNA from synthetic construct)
- Trinucleosome from 4x177 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome stack of the 4x177 nucleosome array containing H1
Resolution: 6.0 Å
EM Method: Single-particle
Fitted PDBs: 7pev
Q-score: 0.224
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (520-mer) (218 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Nucleosome stack from 4x177 nucleosome array (Complex)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Dna (520-mer) (215 kDa, DNA from Homo sapiens)
Nucleosome 1 of the 4x177 nucleosome array containing H1
Resolution: 4.6 Å
EM Method: Single-particle
Fitted PDBs: 7pew
Q-score: 0.29
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (176-mer) (53 kDa, DNA from synthetic construct)
- Nucleosome 1 from 4x177 nucleosome array (Complex)
- Dna (176-mer) (54 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
Nucleosome 2 of the 4x177 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pex
Q-score: 0.267
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Nucleosome 2 from 4x177 nucleosome array (Complex)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (177-mer) (55 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Nucleosome 3 of the 4x177 nucleosome array containing H1
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 7pey
Q-score: 0.281
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosome 3 from 4x177 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Dna (203-mer) (53 kDa, DNA from synthetic construct)
- Dna (202-mer) (52 kDa, DNA from synthetic construct)
Nucleosome 4 of the 4x177 nucleosome array containing H1
Resolution: 7.9 Å
EM Method: Single-particle
Fitted PDBs: 7pez
Q-score: 0.203
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Nucleosome 4 from 4x177 nucleosome array (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (182-mer) (55 kDa, DNA from synthetic construct)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (182-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
Trinucleosome of the 4x177 nucleosome array containing H1
Resolution: 11.0 Å
EM Method: Single-particle
Fitted PDBs: 7pf0
Q-score: 0.101
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histones (Complex from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Dna (563-mer) (166 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Trinucleosome from 4x187 nucleosome array (Complex)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)
- Dna (563-mer) (167 kDa, DNA from synthetic construct)
Nucleosome stack of the 4x187 nucleosome array containing H1
Resolution: 5.1 Å
EM Method: Single-particle
Fitted PDBs: 7pf2
Q-score: 0.217
Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P
Nat Struct Mol Biol (2022) 29 pp. 493-501 [ DOI: doi:10.1038/s41594-022-00768-w Pubmed: 35581345 ]
- Histones (Complex from Homo sapiens)
- Dna (541-mer) (232 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosome stack from 4x187 nucleosome array (Complex)
- Dna (541-mer) (230 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (16 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h1.4 (21 kDa, Protein from Homo sapiens)