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 ]
- Histone h4 (11 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 h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Complex between alc1 and a site-specifically parylated nucleosome (304 kDa, Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Cryo-EM structure of an asymmetric nucleosome (10-N-0) from a Glacios/Falcon3EC
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Widom 601 sequence with 10 additional bp on the strong side (DNA from synthetic construct)
- Histone h2a type 1 (Protein from Xenopus laevis)
- Histone h2b 1.1 (Protein from Xenopus laevis)
- Histone h4 (Protein from Xenopus laevis)
- Histone h3.2 (Protein from Xenopus laevis)
- 601 nucleosome with 10 additional bp (205 kDa, Complex)
Single-particle cryo-EM dataset of the complex between ALC1 and a PARylated nucleosome
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton SJ, Deindl S
eLife (2021) 10 [ DOI: 10.7554/elife.71420 Pubmed: 34486521 ]
Image sets:
- Extracted particles at original pixel size - large set
- Unaligned movies of the complex between ALC1 and a PARylated nucleosome - batch 2
- Unaligned movies of the complex between ALC1 and a PARylated nucleosome - batch 1
- Extracted particles at original pixel size - smaller subset
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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (98 kDa, Protein from Homo sapiens)
- Dna (149-mer) widom 601 sequence (49 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
cryoDRGN graph traversal of the ALC1 - PARylated nucleosome complex particle distribution
Bacic L, Gaullier G, Sabantsev A, Lehmann LC, Brackmann K, Dimakou D, Halic M, Hewitt G, Boulton S, Deindl S
eLife (2021) 10 [ Pubmed: 34486521 DOI: doi:10.7554/eLife.71420 ]
- Alc1/chd1l (Complex from Homo sapiens)
- Alc1/chd1l (Protein from Homo sapiens)
- Histone h3 (Protein from Xenopus laevis)
- Widom 601 sequence (DNA from synthetic construct)
- Histone h2b (Protein from Xenopus laevis)
- Alc1/chd1l bound to a parylated nucleosome (305 kDa, Complex)
- Histone h4 (Protein from Xenopus laevis)
- Widom 601 sequence (Complex from synthetic construct)
- Histone (Complex from Xenopus laevis)
- Histone h2a (Protein from Xenopus laevis)
Lehman 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 [ Pubmed: 33357431 DOI: 10.1016/j.celrep.2020.108529 ]
Image sets:
- Particles of the high-resolution nucleosome class
- Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_2
- Particles of the hexasome class
- Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_3
- Unaligned movies of the nucleosome - ALC1-linker complex - session_1_disk_1
- Unaligned movies of the nucleosome - ALC1-linker complex - session_2_grid_2
- Unaligned movies of the nucleosome - ALC1-linker complex - session_2_grid_1
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 [ Pubmed: 33357431 DOI: doi:10.1016/j.celrep.2020.108529 ]
- Water (18 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 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 h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Histones (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Crosslinked complex of alc1 regulatory linker and the nucleosome (206 kDa, Complex)
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 [ Pubmed: 33357431 DOI: doi:10.1016/j.celrep.2020.108529 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Dna (110-mer) widom 601 sequence (44 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (Complex from Homo sapiens)
- Histones (Complex from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Chromodomain-helicase-dna-binding protein 1-like (4 kDa, Protein from Homo sapiens)
- 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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)