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)
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)
CryoEM structure of the C. sordellii lethal toxin TcsL in complex with SEMA6A
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6wts
Q-score: 0.463
Lee H, Beilhartz GL, Kucharska I, Raman S, Cui H, Lam MHY, Liang H, Rubinstein JL, Schramek D, Julien JP, Melnyk RA, Taipale M
Cell (2020) 182 pp. 345- [ Pubmed: 32589945 DOI: doi:10.1016/j.cell.2020.06.005 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Tcsl (Complex from Paeniclostridium sordellii)
- Sema6a (63 kDa, Protein from Homo sapiens)
- Tcsl (63 kDa, Protein from Paeniclostridium sordellii)
- Sema6a (Complex from Homo sapiens)
- Complex of sema6a with tcsl (Complex)