Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 8xpo
Q-score: 0.554
Jia X, Jing X, Li M, Gao M, Zhong Y, Li E, Liu Y, Li R, Yao G, Liu Q, Zhou M, Hou Y, An L, Hong Y, Li S, Zhang J, Wang W, Zhang K, Gong P, Chiu S
Nat Commun (2024) 15 pp. 10750-10750 [ Pubmed: 39737930 DOI: doi:10.1038/s41467-024-54918-3 ]
- Rna (32-mer) (10 kDa, RNA from synthetic construct)
- Rna (9-mer) (2 kDa, RNA from synthetic construct)
- Rna (14-mer) (4 kDa, RNA from synthetic construct)
- Rna (Complex from synthetic construct)
- [[(2~{r},3~{r},4~{s},5~{r})-4-fluoranyl-5-(5-iodanyl-4-methyl-pyrrolo[2,3-d]pyrimidin-7-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate (633 Da, Ligand)
- Rna-directed rna polymerase l (255 kDa, Protein from Lassa virus Josiah)
- Lassa virus rdrp elongation complex with the ntp form of compound 13b bound in the active site (270 kDa, Complex)
- Lassa virus l protein (Complex from Lassa virus Josiah)
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8j6m
Q-score: 0.587
Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D
Nat Struct Mol Biol (2024) 31 pp. 1095-1104 [ DOI: doi:10.1038/s41594-024-01276-9 Pubmed: 38664565 ]
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Sodium ion (22 Da, Ligand)
- Oleic acid (282 Da, Ligand)
- Cholesterol (386 Da, Ligand)
- T1 (Complex from Homo sapiens)
- Green fluorescent protein,sid1 transmembrane family member 1 (124 kDa, Protein from Homo sapiens)
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8j6o
Q-score: 0.403
Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D
Nat Struct Mol Biol (2024) 31 pp. 1095-1104 [ DOI: doi:10.1038/s41594-024-01276-9 Pubmed: 38664565 ]
- Green fluorescent protein (fragment),sid1 transmembrane family member 2 (124 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- T2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 2.77 Å
EM Method: Single-particle
Fitted PDBs: 8hip
Q-score: 0.596
Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D
Nat Struct Mol Biol (2024) 31 pp. 1095-1104 [ DOI: doi:10.1038/s41594-024-01276-9 Pubmed: 38664565 ]
- Systemic rna interference defective protein 1 (88 kDa, Protein from Homo sapiens)
- [(2~{r})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{z})-octadec-9-enoate (717 Da, Ligand)
- Dsrna transporter complex (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Resolution: 3.71 Å
EM Method: Single-particle
Fitted PDBs: 8hke
Q-score: 0.431
Zhang J, Zhan C, Fan J, Wu D, Zhang R, Wu D, Chen X, Lu Y, Li M, Lin M, Gong J, Jiang D
Nat Struct Mol Biol (2024) 31 pp. 1095-1104 [ DOI: doi:10.1038/s41594-024-01276-9 Pubmed: 38664565 ]
- Systemic rna interference defective protein 1 (88 kDa, Protein from Homo sapiens)
- Dsrna transporter (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Rna (37-mer) (11 kDa, RNA from Homo sapiens)
- Rna (37-mer) (11 kDa, RNA from Homo sapiens)
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)