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 ]
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3s histone deacetylase in complex with histone h3 tail (Complex from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- 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 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)
- Chromatin modification-related protein eaf3 (45 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)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Rpd3s histone deacetylase in complex with nucleosome (680 kDa, Complex from Saccharomyces cerevisiae)
Cryo-EM structure of Eaf3 CHD in complex with nucleosome
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8hxz
Q-score: 0.326
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)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Eaf3 chd in complex with nucleosome (150 kDa, Complex from Saccharomyces)
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 ]
- Rpd3s histone deacetylase in complex with nucleosome (800 kDa, Complex from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Dna (352-mer) (108 kDa, DNA from synthetic construct)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Dna (352-mer) (109 kDa, DNA from synthetic construct)
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 ]
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Di-nucleosome template reverse (108 kDa, DNA from synthetic construct)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3s histone deacetylase in complex with di-nucleosome (550 MDa, Complex)
- Di-nucleosome template foward (107 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- The rpd3s hdac complex (Complex from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Di-nucleosome (400 MDa, Complex from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Resolution: 3.66 Å
EM Method: Single-particle
Fitted PDBs: 8hih
Q-score: 0.202
Shi J, Feng Z, Xu J, Li F, Zhang Y, Wen A, Wang F, Song Q, Wang L, Cui H, Tong S, Chen P, Zhu Y, Zhao G, Wang S, Feng Y, Lin W
PNAS (2023) 120 pp. e2300282120-e2300282120 [ Pubmed: 37216560 DOI: doi:10.1073/pnas.2300282120 ]
- Dna-directed rna polymerase subunit omega (11 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Dna-directed rna polymerase subunit beta (130 kDa, Protein from Mycobacterium tuberculosis)
- Non-template strand dna of amtb promoter (33 kDa, DNA from Mycobacterium tuberculosis)
- Transcriptional regulatory protein (27 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Rna polymerase sigma factor siga (57 kDa, Protein from Mycobacterium tuberculosis H37Rv)
- Magnesium ion (24 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase subunit alpha (37 kDa, Protein from Mycobacterium tuberculosis)
- Template strand dna of amtb promoter (33 kDa, DNA from Mycobacterium tuberculosis)
- Mycobacterium tuberculosis transcription initiation complex with transcription factor glnr (Complex from Mycobacterium tuberculosis)
- Dna-directed rna polymerase subunit beta' (146 kDa, Protein from Mycobacterium tuberculosis)
Rujas E, Kucharska I, Tan YZ, Benlekbir S, Cui H, Zhao T, Wasney GA, Budylowski P, Guvenc F, Newton JC, Sicard T, Semesi A, Muthuraman K, Nouanesengsy A, Aschner CB, Prieto K, Bueler SA, Youssef S, Liao-Chan S, Glanville J, Christie-Holmes N, Mubareka S, Gray-Owen SD, Rubinstein JL, Treanor B, Julien JP
Nat Commun (2021) 12 pp. 3661-3661 [ DOI: doi:10.1038/s41467-021-23825-2 Pubmed: 34135340 ]
- Receptor binding domain of sars-cov-2 spike (Protein from Severe acute respiratory syndrome coronavirus 2)
- Fab fragment of neutralizing antibody 46 (Complex from Homo sapiens)
- Sars-cov-2 receptor binding domain (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab 46 light chain (Protein from Homo sapiens)
- Sars-cov-2 receptor binding domain in complex with the fab fragment of neutralizing antibody 46 (Complex)
- Fab 46 heavy chain (Protein from Homo sapiens)
Rujas E, Kucharska I, Tan YZ, Benlekbir S, Cui H, Zhao T, Wasney GA, Budylowski P, Guvenc F, Newton JC, Sicard T, Semesi A, Muthuraman K, Nouanesengsy A, Aschner CB, Prieto K, Bueler SA, Youssef S, Liao-Chan S, Glanville J, Christie-Holmes N, Mubareka S, Gray-Owen SD, Rubinstein JL, Treanor B, Julien JP
Nat Commun (2021) 12 pp. 3661-3661 [ DOI: doi:10.1038/s41467-021-23825-2 Pubmed: 34135340 ]
- Fab 80 light chain (Protein from Homo sapiens)
- Fab fragment of neutralizing antibody 80 (Complex from Homo sapiens)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab 80 heavy chain (Protein from Homo sapiens)
- Sars-cov-2 spike (Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike in complex with the fab fragment of neutralizing antibody 80 (Complex)
Rujas E, Kucharska I, Tan YZ, Benlekbir S, Cui H, Zhao T, Wasney GA, Budylowski P, Guvenc F, Newton JC, Sicard T, Semesi A, Muthuraman K, Nouanesengsy A, Aschner CB, Prieto K, Bueler SA, Youssef S, Liao-Chan S, Glanville J, Christie-Holmes N, Mubareka S, Gray-Owen SD, Rubinstein JL, Treanor B, Julien JP
Nat Commun (2021) 12 pp. 3661-3661 [ DOI: doi:10.1038/s41467-021-23825-2 Pubmed: 34135340 ]
- Fab 298 heavy chain (Protein from Homo sapiens)
- Sars-cov-2 spike in complex with the fab fragment of neutralizing antibody 298 (Complex)
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab 298 light chain (Protein from Homo sapiens)
- Fab fragment of neutralizing antibody 298 (Complex from Homo sapiens)
- Sars-cov-2 spike (Protein from Severe acute respiratory syndrome coronavirus 2)
Rujas E, Kucharska I, Tan YZ, Benlekbir S, Cui H, Zhao T, Wasney GA, Budylowski P, Guvenc F, Newton JC, Sicard T, Semesi A, Muthuraman K, Nouanesengsy A, Aschner CB, Prieto K, Bueler SA, Youssef S, Liao-Chan S, Glanville J, Christie-Holmes N, Mubareka S, Gray-Owen SD, Rubinstein JL, Treanor B, Julien JP
Nat Commun (2021) 12 pp. 3661-3661 [ DOI: doi:10.1038/s41467-021-23825-2 Pubmed: 34135340 ]
- Sars-cov-2 spike (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab 324 heavy chain (Protein from Homo sapiens)
- Fab 324 light chain (Protein from Homo sapiens)
- Sars-cov-2 spike in complex with the fab fragment of neutralizing antibody 324 (Complex)
- Sars-cov-2 spike (Protein from Severe acute respiratory syndrome coronavirus 2)
- Fab fragment of neutralizing antibody 324 (Complex from Homo sapiens)