Cryo-EM structure of native SWR1 bound to nucleosome (composite structure)
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 9b1e
Q-score: 0.191
Louder RK, Park G, Ye Z, Cha JS, Gardner AM, Lei Q, Ranjan A, Hollmuller E, Stengel F, Pugh BF, Wu C
Cell (2024) 187 pp. 6849-6864.e18 [ Pubmed: 39357520 DOI: doi:10.1016/j.cell.2024.09.007 ]
- Histone h2b (14 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (14 kDa, Protein from Saccharomyces cerevisiae)
- Helicase swr1 (178 kDa, Protein from Saccharomyces cerevisiae W303)
- Dna (214-mer) (65 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Drosophila melanogaster)
- Vacuolar protein sorting-associated protein 72 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Beryllium trifluoride ion (66 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Ruvb-like protein 2 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Ruvb-like protein 1 (91 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Native swr1 bound to nucleosome. (1 MDa, Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Drosophila melanogaster)
- Dna (214-mer) (66 kDa, DNA from synthetic construct)
- Vacuolar protein sorting-associated protein 71 (32 kDa, Protein from Saccharomyces cerevisiae W303)
- Swr1-complex protein 3 (72 kDa, Protein from Saccharomyces cerevisiae W303)
- Actin-like protein arp6 (50 kDa, Protein from Saccharomyces cerevisiae W303)
- Native swr1 complex (Complex from Saccharomyces cerevisiae)
Native SUV420H1 bound to 167-bp nucleosome
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8jhg
Q-score: 0.456
Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W
Cell Discov (2023) 9 pp. 120-120 [ DOI: doi:10.1038/s41421-023-00620-5 Pubmed: 38052811 ]
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Histone-lysine n-methyltransferase kmt5b (41 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Cryo-em structure of the native suv420h1 bound to 167-bp nucleosome (246 kDa, Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
Native SUV420H1 bound to 167-bp nucleosome
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8jhf
Q-score: 0.433
Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W
Cell Discov (2023) 9 pp. 120-120 [ DOI: doi:10.1038/s41421-023-00620-5 Pubmed: 38052811 ]
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- Histone-lysine n-methyltransferase kmt5b (41 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Cryo-em structure of the native suv420h1 bound to 167-bp nucleosome (246 kDa, Complex from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (160-mer) (49 kDa, DNA from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
Cryo-EM map of Eaf3 CHD bound to H3K36me3 nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7yi1
Q-score: 0.572
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ Pubmed: 37468628 DOI: doi:10.1038/s41586-023-06349-1 ]
- Histone h3 (Complex)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Dna (Complex from Saccharomyces cerevisiae S288C)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Eaf3 (Complex from Xenopus laevis)
Cryo-EM map of Rpd3S complex bound to H3K36me3 nucleosome in close state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi4
Q-score: 0.23
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ Pubmed: 37468628 DOI: doi:10.1038/s41586-023-06349-1 ]
- Histone h3 (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (Complex from Xenopus laevis)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
Cryo-EM msp of Rpd3S complex bound to H3K36me3 nucleosome in loose state
Resolution: 3.96 Å
EM Method: Single-particle
Fitted PDBs: 7yi5
Q-score: 0.254
Guan H, Wang P, Zhang P, Ruan C, Ou Y, Peng B, Zheng X, Lei J, Li B, Yan C, Li H
Nature (2023) 620 pp. 669-675 [ Pubmed: 37468628 DOI: doi:10.1038/s41586-023-06349-1 ]
- Histone h3 (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae S288C)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae S288C)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (Complex from Xenopus laevis)
- Sin3/rpd3/eaf3/rco1 (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h4/h2a/h2b 1.1 (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Wisdom 601 dna (167-mer) (51 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae S288C)
- Rpd3s complex with h3k36me3 nucleosome (723 MDa, Complex from Saccharomyces cerevisiae S288C)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
catalytic core of human telomerase holoenzyme
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 7v99
Q-score: 0.247
Wan F, Ding Y, Zhang Y, Wu Z, Li S, Yang L, Yan X, Lan P, Li G, Wu J, Lei M
Cell Res (2021) 31 pp. 1275-1290 [ DOI: doi:10.1038/s41422-021-00586-7 Pubmed: 34782750 ]
- Catalytic core (Complex from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Primer dna (7 kDa, DNA from Homo sapiens)
- Telomerase reverse transcriptase (127 kDa, Protein from Homo sapiens)
- Telomerase rna component (145 kDa, RNA from Homo sapiens)
masked histone region in the catalytic core of human telomerase holoenzyme
Wan F, Ding Y, Zhang Y, Wu Z, Li S, Yang L, Yan X, Lan P, Li G, Wu J, Lei M
Cell Res (2021) 31 pp. 1275-1290 [ DOI: doi:10.1038/s41422-021-00586-7 Pubmed: 34782750 ]
- Telomerase rna component (RNA from Homo sapiens)
- Primer dna (DNA from Homo sapiens)
- Catalytic core (Complex from Homo sapiens)
- Histone h2b type 1-k (Protein from Homo sapiens)
- Telomerase reverse transcriptase (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
The mouse cGAS catalytic domain binding to human assembled nucleosome
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 6x59
Q-score: 0.54
Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P
Nature (2020) 587 pp. 673-677 [ Pubmed: 32911481 DOI: doi:10.1038/s41586-020-2749-z ]
- Cgas-nucleosome complex (Complex from Homo sapiens)
- Dna (45 kDa, DNA from Homo sapiens)
- Dna (45 kDa, DNA from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (43 kDa, Protein from Mus musculus)
The mouse cGAS catalytic domain binding to human nucleosome that purified from HEK293T cells
Resolution: 4.36 Å
EM Method: Single-particle
Fitted PDBs: 6x5a
Q-score: 0.265
Zhao B, Xu P, Rowlett CM, Jing T, Shinde O, Lei Y, West AP, Liu WR, Li P
Nature (2020) 587 pp. 673-677 [ Pubmed: 32911481 DOI: doi:10.1038/s41586-020-2749-z ]
- Dna (natural) (45 kDa, DNA from Homo sapiens)
- Cgas-nucleosome complex (Complex from Homo sapiens)
- Histone h2b type 1-c/e/f/g/i (13 kDa, Protein from Homo sapiens)
- Histone h3.2 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1 (13 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Cyclic gmp-amp synthase (43 kDa, Protein from Mus musculus)
- Dna (natural) (45 kDa, DNA from Homo sapiens)