Cryo-EM structure of ALC1 bound to an asymmetric, site-specifically PARylated nucleosome
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8b0a
Q-score: 0.483
Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S
Nat Commun (2024) 15 pp. 1000-1000 [ Pubmed: 38307862 DOI: doi:10.1038/s41467-024-45237-8 ]
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Complex between alc1 and a site-specifically parylated nucleosome (304 kDa, Complex from Homo sapiens)
Cryo-EM structure of ALC1/CHD1L bound to a PARylated nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7otq
Q-score: 0.282
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton S, Deindl S, Workman JL
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Nucleosome in interphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.38 Å
EM Method: Single-particle
Fitted PDBs: 7kbd
Q-score: 0.489
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Dna (151-mer) (46 kDa, DNA from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nucleosome in interphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
Nucleosome isolated from metaphase chromosome formed in Xenopus egg extract (oligo fraction)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7kbe
Q-score: 0.445
Arimura Y, Shih RM, Froom R, Funabiki H
Mol Cell (2021) 81 pp. 4377- [ Pubmed: 34478647 DOI: doi:10.1016/j.molcel.2021.08.010 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (47 kDa, DNA from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (157-mer) (48 kDa, DNA from Xenopus laevis)
- Nucleosome isolated from metaphase chromosome formed in xenopus egg extract (oligo fraction) (Complex from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6zhx
Q-score: 0.625
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Crosslinked complex of alc1 regulatory linker and the nucleosome (206 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Dna (145-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Water (18 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6zhy
Q-score: 0.516
Lehmann LC, Bacic L, Hewitt G, Brackmann K, Sabantsev A, Gaullier G, Pytharopoulou S, Degliesposti G, Okkenhaug H, Tan S, Costa A, Skehel JM, Boulton SJ, Deindl S
Cell Rep (2020) 33 pp. 108529-108529 [ DOI: doi:10.1016/j.celrep.2020.108529 Pubmed: 33357431 ]
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- A hexasome (nucleosome lacking one of the two h2a-h2b dimers) with its acidic patch bound by the alc1 linker regulatory region. (170 kDa, Complex)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histones (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
Nucleosome-CHD4 complex structure (single CHD4 copy)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6ryr
Q-score: 0.52
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56178 Pubmed: 32543371 ]
- Zinc ion (65 Da, Ligand)
- Nucleosome-chd4 complex (Complex)
- Chd4 (Complex from Homo sapiens)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (149-mer) (46 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)
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
- Nucleosome (Complex from Xenopus laevis)
Nucleosome-CHD4 complex structure (two CHD4 copies)
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6ryu
Q-score: 0.342
Farnung L, Ochmann M, Cramer P
eLife (2020) 9 [ DOI: doi:10.7554/eLife.56178 Pubmed: 32543371 ]
- Zinc ion (65 Da, Ligand)
- Nucleosome-chd4 complex (Complex)
- Histone (Complex from Xenopus laevis)
- Dna (149-mer) (45 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (149-mer) (46 kDa, DNA from synthetic construct)
- Chromodomain-helicase-dna-binding protein 4 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Magnesium ion (24 Da, Ligand)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Chromodomain-helicase-dna-binding protein 4,chd4,chromodomain-helicase-dna-binding protein 4 (219 kDa, Protein from Homo sapiens)
The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 6jyl
Q-score: 0.452
Yan L, Wu H, Li X, Gao N, Chen Z
Nat Struct Mol Biol (2019) 26 pp. 258-266 [ DOI: doi:10.1038/s41594-019-0199-9 Pubmed: 30872815 ]
- Iswi (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
- Dna (Complex from Escherichia coli K-12)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Iswi-nucleosome-crosslinked (300 kDa, Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, Protein from Escherichia coli K-12)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))