Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp.
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 9gd1
Q-score: 0.332
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ Pubmed: 39270644 DOI: doi:10.1016/j.molcel.2024.08.022 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (261-mer) (81 kDa, DNA from synthetic construct)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp.
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 9gd2
Q-score: 0.295
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ Pubmed: 39270644 DOI: doi:10.1016/j.molcel.2024.08.022 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (248-mer) (77 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (248-mer) (76 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. (Complex from Xenopus laevis)
Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA.
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 9gd3
Q-score: 0.465
Engeholm M, Roske JJ, Oberbeckmann E, Dienemann C, Lidschreiber M, Cramer P, Farnung L
Mol Cell (2024) 84 pp. 3423- [ Pubmed: 39270644 DOI: doi:10.1016/j.molcel.2024.08.022 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
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 [ DOI: doi:10.1021/jacs.2c13512 Pubmed: 36930461 ]
- Histone h4 (11 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)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Sirt6 bound to h3k9ac (Complex)
- Dna (148-mer) (56 kDa, DNA from synthetic construct)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Nad-dependent protein deacylase sirtuin-6 (39 kDa, Protein from Homo sapiens)
- Dna (148-mer) (57 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
Structure of nucleosome-Chd1 complex
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 5o9g
Q-score: 0.018
Farnung L, Vos SM, Wigge C, Cramer P
Nature (2017) 550 pp. 539-542 [ Pubmed: 29019976 DOI: doi:10.1038/nature24046 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Protein-nucleic acid complex (Complex)
- Dna (162-mer) (64 kDa, DNA from synthetic construct)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (162-mer) (64 kDa, DNA from synthetic construct)
- Protein-nucleic acid complex (Complex from synthetic construct)
- Protein-nucleic acid complex (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Protein-nucleic acid complex (Complex from Saccharomyces cerevisiae S288c)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288c)