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 ]
- Potassium ion (39 Da, Ligand)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein 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 ]
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 5-dna (45 kDa, DNA from Homo sapiens)
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 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
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 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of a SIN3/HDAC complex from budding yeast
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8hpo
Q-score: 0.492
Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C
Nat Struct Mol Biol (2023) [ DOI: doi:10.1038/s41594-023-00975-z Pubmed: 37081318 ]
- Transcriptional regulatory protein rxt2 (48 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein rxt3 (33 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein pho23 (37 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein sap30 (23 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein ume1 (51 kDa, Protein from Baker's yeast)
- The rpd3l complex (Complex from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Phosphothreonine (199 Da, Ligand)
- Transcriptional regulatory protein dep1 (47 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Histone deacetylase rpd3 (49 kDa, Protein from Baker's yeast)
- Histone deacetylase rpd3 (48 kDa, Protein from Baker's yeast)
- Transcriptional regulatory protein sds3 (37 kDa, Protein from Baker's yeast)