SWR1-nucleosome complex in configuration 1
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qku
Q-score: 0.363
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ Pubmed: 39506114 DOI: doi:10.1038/s41586-024-08152-y ]
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (177-mer) (54 kDa, DNA from synthetic construct)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
SWR1-nucleosome complex in configuration 2
Resolution: 4.7 Å
EM Method: Single-particle
Fitted PDBs: 8qkv
Q-score: 0.185
Girvan P, Jalal ASB, McCormack EA, Skehan MT, Knight CL, Wigley DB, Rueda DS
Nature (2024) 636 pp. 251-257 [ Pubmed: 39506114 DOI: doi:10.1038/s41586-024-08152-y ]
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (194-mer) (60 kDa, DNA from synthetic construct)
- Histone h2a.2 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (194-mer) (59 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 72 (21 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8qyv
Q-score: 0.324
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ Pubmed: 39226902 DOI: doi:10.1016/j.molcel.2024.08.015 ]
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Dna (118-mer) (36 kDa, DNA from synthetic construct)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome complex (Complex from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8qz0
Q-score: 0.293
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ Pubmed: 39226902 DOI: doi:10.1016/j.molcel.2024.08.015 ]
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Histone h2a.z-specific chaperone chz1 (17 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (113-mer) (36 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Swr1-complex protein 5 (34 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-hexasome-dimer complex (Complex from Saccharomyces cerevisiae S288C)
- Histone h2a.z (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
SWR1 lacking Swc5 subunit in complex with hexasome
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9fbw
Q-score: 0.193
Jalal ASB, Girvan P, Chua EYD, Liu L, Wang S, McCormack EA, Skehan MT, Knight CL, Rueda DS, Wigley DB
Mol Cell (2024) 84 pp. 3871- [ Pubmed: 39226902 DOI: doi:10.1016/j.molcel.2024.08.015 ]
- Histone h3 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ruvb-like protein 1 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1 lacking swc5 subunit in complex with hexasome (Complex from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae S288C)
- Helicase swr1 (174 kDa, Protein from Saccharomyces cerevisiae S288C)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (112-mer) (34 kDa, DNA from synthetic construct)
- Dna (112-mer) (34 kDa, DNA from synthetic construct)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Histone h2b.1 (14 kDa, Protein from Saccharomyces cerevisiae S288C)
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- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (261-mer) (81 kDa, DNA from synthetic construct)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
- Dna (261-mer) (80 kDa, DNA from synthetic construct)
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- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (248-mer) (76 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (248-mer) (77 kDa, DNA from synthetic construct)
- Hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. (Complex from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein 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- [ DOI: doi:10.1016/j.molcel.2024.08.022 Pubmed: 39270644 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Chromo domain-containing protein 1 (168 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (231-mer) (71 kDa, DNA from synthetic construct)
- Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp (Complex from Saccharomyces cerevisiae S288C)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (14 kDa, Protein from Xenopus laevis)
Structure of Bre1-nucleosome complex - state1
Resolution: 3.47 Å
EM Method: Single-particle
Fitted PDBs: 8t3y
Q-score: 0.503
Nat Struct Mol Biol (2023) 30 pp. 1623-1627 [ Pubmed: 37872231 DOI: doi:10.1038/s41594-023-01137-x ]
- 601 dna strand 2 (45 kDa, DNA from synthetic construct)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Bre1-nucleosome complex (Complex from Saccharomyces cerevisiae)
- E3 ubiquitin-protein ligase bre1 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 601 dna strand 1 (44 kDa, DNA from synthetic construct)
Cryo-EM structure of ISW1a-dinucleosome
Resolution: 5.4 Å
EM Method: Single-particle
Fitted PDBs: 7x3t
Q-score: 0.192
Li L, Chen K, Sia Y, Hu P, Ye Y, Chen Z
Nat Struct Mol Biol (2024) 31 pp. 266-274 [ DOI: doi:10.1038/s41594-023-01174-6 Pubmed: 38177688 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (343-mer) (108 kDa, DNA from synthetic construct)
- Isw1a-dinucleosome (392 MDa, Complex from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna(343-mer) (109 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)