Rpd3S in complex with 187bp nucleosome
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8kd2
Q-score: 0.35
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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Dna (Complex from synthetic construct)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Dna (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- 187bp dna (57 kDa, DNA from synthetic construct)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Dna (Complex)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
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 h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (57 kDa, DNA from synthetic construct)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp (187bp/mla) class2 (Complex)
- 187bp dna (Complex from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone (Complex from Xenopus laevis)
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 ]
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Dna (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- 187bp dna (58 kDa, DNA from synthetic construct)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8kd7
Q-score: 0.324
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)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Alternative deacetylation state of rpd3s-ncp(167bp/mla) (Complex)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Eaf3-rpd3-sin3 (Complex from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 167bp dna (Complex from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)