Do data resources managed by EMBL-EBI and our collaborators make a difference to your work? Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research. We appreciate your responses prior to closing of the survey on Monday 17th June.
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 [ DOI: doi:10.1126/sciadv.adk7678 Pubmed: 38598631 ]
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- Unclear peptide (487 Da, Protein from Saccharomyces cerevisiae)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 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 ]
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- 3-dna (45 kDa, DNA from Homo sapiens)
- 5-dna (45 kDa, DNA from Homo sapiens)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- The rpd3s complex (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Calcium ion (40 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Rco1 (515 Da, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Dna (176-mer) (66 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Rpd3s bound to h3k36cme3 nucleosome (Complex)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Histone n-terminal tail (657 Da, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (14 kDa, Protein from Xenopus laevis)
- Dna (176-mer) (63 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Dna (352-mer) (108 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3s histone deacetylase in complex with nucleosome (680 kDa, Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- Dna (352-mer) (108 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Rpd3s histone deacetylase in complex with nucleosome (800 kDa, Complex from Saccharomyces cerevisiae)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome
Resolution: 7.6 Å
EM Method: Single-particle
Fitted PDBs: 8jho
Q-score: 0.067
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 di-nucleosome (550 MDa, Complex)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Di-nucleosome template foward (107 kDa, DNA from synthetic construct)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Di-nucleosome template reverse (108 kDa, DNA from synthetic construct)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Di-nucleosome (400 MDa, Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- The rpd3s hdac complex (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
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 deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
- Dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- 187bp dna (58 kDa, DNA from synthetic construct)
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 deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone (Complex from Xenopus laevis)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Dna (Complex)