Tomogram of chromatin fibers with 50 repeat of nucleosomes and a long NRL of 200 bp in vitro
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 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae)
- Complex of nua4 hat module and nucleosome (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- H4 (11 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae)
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 [ Pubmed: 36198799 DOI: doi:10.1038/s41586-022-05303-x ]
- Dna (207-mer) (64 kDa, DNA from Saccharomyces cerevisiae)
- Actin-related protein 4 (54 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Actin (41 kDa, Protein from Saccharomyces cerevisiae S288C)
- Nua4 bound to the nucleosome (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein yng2 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcription-associated protein 1 (433 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf1 (133 kDa, Protein from Saccharomyces cerevisiae S288C)
- Epl1 arginine anchor (1 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf6 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone acetyltransferase esa1 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Swr1-complex protein 4 (55 kDa, Protein from Saccharomyces cerevisiae S288C)
- Carboxymethyl coenzyme *a (825 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Enhancer of polycomb-like protein 1 (96 kDa, Protein from Saccharomyces cerevisiae S288C)
- Dna (207-mer) (63 kDa, DNA from Saccharomyces cerevisiae)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Structure of Snf2-nucleosome complex at shl2 in ADP BeFx state
Resolution: 4.31 Å
EM Method: Single-particle
Fitted PDBs: 5z3u
Q-score: 0.372
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ Pubmed: 30867599 DOI: doi:10.1038/s41586-019-1029-2 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Complex of snf2 and nucleosome in adp befx state (300 kDa, Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
Resolution: 4.22 Å
EM Method: Single-particle
Fitted PDBs: 5z3v
Q-score: 0.356
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ Pubmed: 30867599 DOI: doi:10.1038/s41586-019-1029-2 ]
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Beryllium trifluoride ion (66 Da, Ligand)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Complex of snf2 and nucleosome in adp befx state (300 kDa, Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
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 [ Pubmed: 30872815 DOI: doi:10.1038/s41594-019-0199-9 ]
- Iswi (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Dna (Complex from Escherichia coli K-12)
- Iswi-nucleosome-crosslinked (300 kDa, Complex)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Iswi chromatin-remodeling complex atpase isw1 (123 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Beryllium trifluoride ion (66 Da, Ligand)
- Nucleosome (Complex from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from Escherichia coli K-12)
- Dna (167-mer) (51 kDa, Protein from Escherichia coli K-12)
Structure of Snf2-nucleosome complex in apo state
Resolution: 4.31 Å
EM Method: Single-particle
Fitted PDBs: 5z3l
Q-score: 0.261
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ Pubmed: 30867599 DOI: doi:10.1038/s41586-019-1029-2 ]
- Complex of snf2 and nucleosome in apo state (300 kDa, Complex from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae)
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
Structure of Snf2-nucleosome complex in ADP state
Resolution: 3.62 Å
EM Method: Single-particle
Fitted PDBs: 5z3o
Q-score: 0.349
Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z
Nature (2019) 567 pp. 409-413 [ DOI: doi:10.1038/s41586-019-1029-2 Pubmed: 30867599 ]
- Dna (167-mer) (51 kDa, DNA from synthetic construct)
- Magnesium ion (24 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Complex of snf2 and nucleosome in adp state (300 kDa, Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Transcription regulatory protein snf2 (85 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (167-mer) (51 kDa, DNA from synthetic construct)