Rpd3S in complex with nucleosome with H3K36MLA modification, H3K9Q mutation and 187bp DNA
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd3
Q-score: 0.376
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ Pubmed: 37666978 DOI: doi:10.1038/s41422-023-00869-1 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Histone (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8kd4
Q-score: 0.373
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ Pubmed: 37666978 DOI: doi:10.1038/s41422-023-00869-1 ]
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd5
Q-score: 0.378
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ Pubmed: 37666978 DOI: doi:10.1038/s41422-023-00869-1 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- H3/h4 deacetylation state of rpd3s-ncp (187bp/mla) class2 (Complex)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (Complex from synthetic construct)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kd6
Q-score: 0.311
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ Pubmed: 37666978 DOI: doi:10.1038/s41422-023-00869-1 ]
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the human INO80 complex bound to a WT nucleosome
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7zi4
Q-score: 0.462
Vance NR, Ayala R, Willhoft O, Tvardovskiy A, McCormack EA, Bartke T, Zhang X, Wigley DB
To Be Published
- Ino80 complex subunit c (20 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Dna (158-mer) (48 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Ino80 complex subunit b (38 kDa, Protein from Homo sapiens)
- Chromatin-remodeling atpase ino80 (177 kDa, Protein from Homo sapiens)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Complex of human ino80core bound to a wt nucleosome (1 MDa, Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
Yeast COMPASS in complex with a ubiquitinated nucleosome
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 6ven
Q-score: 0.449
Worden EJ, Zhang X, Wolberger C
eLife (2020) 9 [ DOI: doi:10.7554/eLife.53199 Pubmed: 31922488 ]
- Zinc ion (65 Da, Ligand)
- Compass component swd3 (34 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 601 dna (146-mer) (44 kDa, DNA from synthetic construct)
- Histone-lysine n-methyltransferase, h3 lysine-4 specific (41 kDa, Protein from Saccharomyces cerevisiae)
- Compass component sdc1 (19 kDa, Protein from Saccharomyces cerevisiae)
- Complex between yeast compass and a ubiquitinated nucleosome (Complex)
- Compass component spp1 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone h3.2 (15 kDa, Protein from Xenopus laevis)
- Yeast compass (Complex from Saccharomyces cerevisiae)
- 601 dna (146-mer) (45 kDa, DNA from synthetic construct)
- Compass component bre2 (58 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1 (13 kDa, Protein from Xenopus laevis)
- S-adenosylmethionine (398 Da, Ligand)
- Ubiquitin (9 kDa, Protein from Homo sapiens)
- Ubiquitinated nucleosome (Complex from Xenopus laevis)
- Compass component swd1 (48 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the human INO80 complex bound to nucleosome
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6hts
Q-score: 0.181
Ayala R, Willhoft O, Aramayo RJ, Wilkinson M, McCormack EA, Ocloo L, Wigley DB, Zhang X
Nature (2018) 556 pp. 391-395 [ Pubmed: 29643506 DOI: doi:10.1038/s41586-018-0021-6 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Actin-related protein 5 (68 kDa, Protein from Homo sapiens)
- Ino80 complex subunit b (38 kDa, Protein from synthetic construct)
- Ruvb-like 2 (51 kDa, Protein from Homo sapiens)
- Dna helicase ino80 (146 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (13 kDa, Protein from Homo sapiens)
- Dna (142-mer) (62 kDa, DNA from synthetic construct)
- Dna (142-mer) (61 kDa, DNA from synthetic construct)
- Human ino80 (Complex from synthetic construct)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Ruvb-like 1 (50 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Complex of core human ino80 with nucleosome (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Nucleosome (Complex from Homo sapiens)
- Histone subunits (Complex from Homo sapiens)