Rpd3S histone deacetylase complex
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8kc7
Q-score: 0.375
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 deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase complex rpd3s in its apo form (527 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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 h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Dna (Complex from synthetic construct)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
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)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex 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)
- Zinc ion (65 Da, Ligand)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone (Complex from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 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)
- Histone h2a (13 kDa, Protein 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 sin3 (176 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 ]
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex)
- 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)
- Zinc ion (65 Da, Ligand)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- Histone (Complex from Xenopus laevis)
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)
- Alternative deacetylation state of rpd3s-ncp(167bp/mla) (Complex)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 167bp dna (Complex from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Eaf3-rpd3-sin3 (Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (51 kDa, DNA from synthetic construct)
Resolution: 2.57 Å
EM Method: Single-particle
Fitted PDBs: 8h0x
Q-score: 0.614
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Resolution: 2.85 Å
EM Method: Single-particle
Fitted PDBs: 8h0y
Q-score: 0.59
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8h0z
Q-score: 0.56
Zhang X, Li Z, Zhang Y, Liu Y, Wang J, Liu B, Chen Q, Wang Q, Fu L, Wang P, Zhong X, Jin L, Yan Q, Chen L, He J, Zhao J, Xiong X
Life Sci Alliance (2023) 6 [ Pubmed: 37402591 DOI: doi:10.26508/lsa.202201796 ]
- Biliverdine ix alpha (582 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-1 spike protein (410 kDa, Complex from Severe acute respiratory syndrome coronavirus)
- Linoleic acid (280 Da, Ligand)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus)