Copper-transporting ATPase HMA4 in E1 state apo
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8q73
Q-score: 0.259
Guo Z, Oradd F, Bagenholm V, Gronberg C, Ma JF, Ott P, Wang Y, Andersson M, Pedersen PA, Wang K, Gourdon P
Nat Commun (2024) 15 pp. 2690-2690 [ Pubmed: 38538615 DOI: doi:10.1038/s41467-024-47001-4 ]
Copper-transporting ATPase HMA4 in E1 state with Cu
Resolution: 3.68 Å
EM Method: Single-particle
Fitted PDBs: 8q74
Q-score: 0.282
Guo Z, Oradd F, Bagenholm V, Gronberg C, Ma JF, Ott P, Wang Y, Andersson M, Pedersen PA, Wang K, Gourdon P
Nat Commun (2024) 15 pp. 2690-2690 [ Pubmed: 38538615 DOI: doi:10.1038/s41467-024-47001-4 ]
Copper-transporting ATPase HMA4 in E2P state with AlF
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8q75
Q-score: 0.368
Guo Z, Oradd F, Bagenholm V, Gronberg C, Ma JF, Ott P, Wang Y, Andersson M, Pedersen PA, Wang K, Gourdon P
Nat Commun (2024) 15 pp. 2690-2690 [ Pubmed: 38538615 DOI: doi:10.1038/s41467-024-47001-4 ]
- Copper-transporting atpase hma4 (94 kDa, Protein from Oryza sativa Japonica Group)
- Copper-transporting atpase hma4 from oryza sativa subsp. japonica (Complex from Oryza sativa Japonica Group)
- Magnesium ion (24 Da, Ligand)
- Tetrafluoroaluminate ion (102 Da, Ligand)
Copper-transporting ATPase HMA4 in E2P state with BeF
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8q76
Q-score: 0.33
Guo Z, Oradd F, Bagenholm V, Gronberg C, Ma JF, Ott P, Wang Y, Andersson M, Pedersen PA, Wang K, Gourdon P
Nat Commun (2024) 15 pp. 2690-2690 [ Pubmed: 38538615 DOI: doi:10.1038/s41467-024-47001-4 ]
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)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 7yrd
Q-score: 0.484
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z
Mol Cell (2023) 83 pp. 2884-2895.e7 [ Pubmed: 37536340 DOI: doi:10.1016/j.molcel.2023.07.001 ]
- Histone h2b 1.1 (10 kDa, Protein from Xenopus laevis)
- Histone h2a.z (12 kDa, Protein from Homo sapiens)
- S-adenosylmethionine (398 Da, Ligand)
- [histone h4]-n-methyl-l-lysine20 n-methyltransferase kmt5b (32 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (146-mer) (45 kDa, DNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone methyltransferase and nucleosome complex (Complex from Homo sapiens)
- Histone h3.2 (12 kDa, Protein from Xenopus laevis)
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)