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)
Cryo-EM structure of IOC3-N2 nucleosome
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7x3v
Q-score: 0.502
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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Iswi one complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Ioc3 (Complex)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Dna (Complex from Saccharomyces cerevisiae S288c)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- N2 nucleosome (Complex)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of ISW1-N1 nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7x3w
Q-score: 0.489
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)
- Dna (Complex)
- N2 nucleosome (Complex from Saccharomyces cerevisiae S288c)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ioc3 (Complex)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Cryo-EM structure of N1 nucleosome-RA
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7x3x
Q-score: 0.44
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 ]
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Ioc3-n2 nucleosome (392 MDa, Complex from Xenopus laevis)
- Ioc3 (Complex)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- N2 nucleosome (Complex)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (Complex from Saccharomyces cerevisiae S288C)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
NuA4 HAT module bound to the nucleosome
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7vvu
Q-score: 0.314
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ DOI: doi:10.1038/s41586-022-05303-x Pubmed: 36198799 ]
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae)
- H4 (11 kDa, Protein from Xenopus laevis)
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae)
- Complex of nua4 hat module and nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
Resolution: 8.8 Å
EM Method: Single-particle
Fitted PDBs: 7vvz
Q-score: 0.108
Qu K, Chen K, Wang H, Li X, Chen Z
Nature (2022) 610 pp. 569-574 [ DOI: doi:10.1038/s41586-022-05303-x Pubmed: 36198799 ]
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Epl1 arginine anchor (1 kDa, Protein from Saccharomyces cerevisiae)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nua4 bound to the nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
The structure of ALC1 bound to the nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7enn
Q-score: 0.567
Nat Commun (2021) 12 pp. 4057-4057 [ DOI: doi:10.1038/s41467-021-24320-4 Pubmed: 34210977 ]
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Histone (Complex from Xenopus laevis)
- Chromodomain-helicase-dna-binding protein 1-like (101 kDa, Protein from Homo sapiens)
- Alc1 (Complex from Homo sapiens)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- The structure of alc1 bound to the nucleosome (Complex)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
The ClassA RSC-Nucleosome Complex
Resolution: 7.13 Å
EM Method: Single-particle
Fitted PDBs: 6kw3
Q-score: 0.086
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
The ClassB RSC-Nucleosome Complex
Resolution: 7.55 Å
EM Method: Single-particle
Fitted PDBs: 6kw4
Q-score: 0.099
Ye Y, Wu H, Chen K, Clapier CR, Verma N, Zhang W, Deng H, Cairns BR, Gao N, Chen Z
Science (2019) 366 pp. 838-843 [ Pubmed: 31672915 DOI: doi:10.1126/science.aay0033 ]
- Chromatin structure-remodeling complex protein rsc8 (63 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear protein sth1/nps1 (156 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Actin-related protein 7 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- Actin-like protein arp9 (53 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna 167 (51 kDa, DNA from Homo sapiens)
- Chromatin structure-remodeling complex protein rsc30 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc3 (101 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (13 kDa, Protein from Xenopus laevis)
- Regulator of ty1 transposition protein 102 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc9 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex protein rsc58 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rsc (Complex from Saccharomyces cerevisiae S288c)
- Chromatin structure-remodeling complex subunit sfh1 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Chromatin structure-remodeling complex protein rsc6 (54 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc2 (102 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc4 (72 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- High temperature lethal protein 1 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin structure-remodeling complex subunit rsc7 (49 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))