Rpd3S histone deacetylase complex
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8kc7
Q-score: 0.375
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase complex rpd3s in its apo form (527 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Linker tightening state of rpd3s-ncp(187bp) (Complex)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Dna (Complex from synthetic construct)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3k9 deacetylation state of rpd3s-ncp (187bp/mla/k9q) (Complex)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class1
Resolution: 2.93 Å
EM Method: Single-particle
Fitted PDBs: 8kd4
Q-score: 0.373
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla)class1 (Complex)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 187bp dna (57 kDa, DNA from synthetic construct)
- Rpd3-sin3-rco1-eaf3 (Complex from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class2
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8kd5
Q-score: 0.378
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (78 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (Complex from synthetic construct)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 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)
- Transcriptional regulatory protein sin3 (176 kDa, Protein from Saccharomyces cerevisiae)
- H3/h4 deacetylation state of rpd3s-ncp (187bp/mla) class2 (Complex)
- Histone (Complex from Xenopus laevis)
Rpd3S in complex with nucleosome with H3K36MLA modification and 187bp DNA, class3
Resolution: 3.07 Å
EM Method: Single-particle
Fitted PDBs: 8kd6
Q-score: 0.311
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Rpd3-sin3-eaf3-rco1 (Complex from Saccharomyces cerevisiae)
- Histone (Complex from Xenopus laevis)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- 187bp dna (58 kDa, DNA from synthetic construct)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 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)
- H3/h4 deacetylation state of rpd3s-ncp(187bp/mla) class3 (Complex)
- Dna (Complex)
Rpd3S in complex with nucleosome with H3K36MLA modification and 167bp DNA
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 8kd7
Q-score: 0.324
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 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Eaf3-rpd3-sin3 (Complex from Saccharomyces cerevisiae)
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae)
- Alternative deacetylation state of rpd3s-ncp(167bp/mla) (Complex)
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b 1.1 (13 kDa, Protein from Xenopus laevis)
- 167bp dna (51 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- 167bp dna (Complex from synthetic construct)
- Histone (Complex from Xenopus laevis)
Cryo-EM structure of human Alpha-fetoprotein
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 7yim
Q-score: 0.484
Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H
Nat Methods (2023) 20 pp. 123-130 [ DOI: doi:10.1038/s41592-022-01693-y Pubmed: 36522503 ]
- Alpha-fetoprotein with no symmetry (67 kDa, Complex from Homo sapiens)
- Alpha-fetoprotein (68 kDa, Protein from Homo sapiens)
cryo-EM structure of hemoglobin
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7xgy
Q-score: 0.407
Zheng L, Liu N, Gao X, Zhu W, Liu K, Wu C, Yan R, Zhang J, Gao X, Yao Y, Deng B, Xu J, Lu Y, Liu Z, Li M, Wei X, Wang HW, Peng H
Nat Methods (2023) 20 pp. 123-130 [ DOI: doi:10.1038/s41592-022-01693-y Pubmed: 36522503 ]
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Hemoglobin (Complex from Homo sapiens)
- Hemoglobin subunit beta (16 kDa, Protein from Homo sapiens)
- Hemoglobin subunit alpha (15 kDa, Protein from Homo sapiens)
S protein of Delta variant in complex with ZWD12
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7wwl
Q-score: 0.444
Chi X, Guo Y, Zhang G, Sun H, Zhang J, Li M, Chen Z, Han J, Zhang Y, Zhang X, Fan P, Zhang Z, Wang B, Zai X, Han X, Hao M, Fang T, Xu J, Wu S, Chen Y, Fang Y, Dong Y, Sun B, Zhang J, Li J, Zhao G, Yu C, Zhou Q, Chen W
Signal Transduct Target Ther (2022) 7 pp. 139-139 [ Pubmed: 35478188 DOI: doi:10.1038/s41392-022-00987-z ]
- S protein of delta variant in complex with zwd12 (Complex)
- Heavy chain of zwd12 (13 kDa, Protein from Homo sapiens)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S protein of delta variant (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zwd12 (Complex from Homo sapiens)
- Light chain of zwd12 (11 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)