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Cryo-EM structure of the Rpd3S complex from budding yeast
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8w9c
Q-score: 0.423
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ Pubmed: 38598631 DOI: doi:10.1126/sciadv.adk7678 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8w9d
Q-score: 0.263
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ Pubmed: 38598631 DOI: doi:10.1126/sciadv.adk7678 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 2
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8w9e
Q-score: 0.188
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ Pubmed: 38598631 DOI: doi:10.1126/sciadv.adk7678 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 3
Resolution: 4.4 Å
EM Method: Single-particle
Fitted PDBs: 8w9f
Q-score: 0.156
Sci Adv (2024) 10 pp. eadk7678-eadk7678 [ Pubmed: 38598631 DOI: doi:10.1126/sciadv.adk7678 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the Rpd3S core complex
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8ihn
Q-score: 0.48
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h3 (2 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Zinc ion (65 Da, Ligand)
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8iht
Q-score: 0.345
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
Rpd3S bound to an H3K36Cme3 modified nucleosome
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8tof
Q-score: 0.464
Nat Commun (2023) 14 pp. 8128-8128 [ Pubmed: 38065958 DOI: doi:10.1038/s41467-023-43968-8 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
- Zinc ion (65 Da, Ligand)
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the histone deacetylase complex Rpd3S
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8hxx
Q-score: 0.453
Nat Struct Mol Biol (2023) 30 pp. 1893-1901 [ Pubmed: 37798513 DOI: doi:10.1038/s41594-023-01121-5 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3s histone deacetylase in complex with histone h3 tail (Complex from Saccharomyces cerevisiae)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hxy
Q-score: 0.44
Nat Struct Mol Biol (2023) 30 pp. 1893-1901 [ Pubmed: 37798513 DOI: doi:10.1038/s41594-023-01121-5 ]
- Rpd3s histone deacetylase in complex with nucleosome (680 kDa, Complex from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (352-mer) (108 kDa, DNA from synthetic construct)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8hy0
Q-score: 0.463
Nat Struct Mol Biol (2023) 30 pp. 1893-1901 [ Pubmed: 37798513 DOI: doi:10.1038/s41594-023-01121-5 ]
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (352-mer) (108 kDa, DNA from synthetic construct)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rpd3s histone deacetylase in complex with nucleosome (800 kDa, Complex from Saccharomyces cerevisiae)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)