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 complex rpd3s in its apo form (527 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein sin3 (157 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 ]
- Dna (Complex from synthetic construct)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- 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)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
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)
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 ]
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Histone (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- 167bp dna (Complex from synthetic construct)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Alternative deacetylation state of rpd3s-ncp(167bp/mla) (Complex)
- Eaf3-rpd3-sin3 (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
Type VI secretion system effector RhsP in its post-autoproteolysis and monomeric form
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8h8a
Q-score: 0.49
Tang L, Dong S, Rasheed N, Wu HW, Zhou N, Li H, Wang M, Zheng J, He J, Chao WCH
Cell Rep (2022) 41 pp. 111732-111732 [ Pubmed: 36476863 DOI: doi:10.1016/j.celrep.2022.111732 ]
- Putative rhs-family protein (131 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- Type vi secretion system effector rhsp in its post-autoproteolysis form (Complex from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- C-terminal peptide from putative rhs-family protein (28 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Type VI secretion system effector RhsP in its pre-autoproteolysis and monomeric form
Type VI secretion system effector RhsP in its post-autoproteolysis and dimeric form
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8h8c
Q-score: 0.446
Tang L, Dong S, Rasheed N, Wu HW, Zhou N, Li H, Wang M, Zheng J, He J, Chao WCH
Cell Rep (2022) 41 pp. 111732-111732 [ Pubmed: 36476863 DOI: doi:10.1016/j.celrep.2022.111732 ]
- Putative rhs-family protein (131 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- Type vi secretion system effector rhsp in its post-autoproteolysis form (Complex from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- C-terminal peptide from putative rhs-family protein (28 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))