Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 12
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8rox
Q-score: 0.452
Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnstrom M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI
J Med Chem (2024) 67 pp. 5538-5566 [ Pubmed: 38513086 DOI: doi:10.1021/acs.jmedchem.3c02136 ]
- Complex of the human ddb1-dda1-dcaf15 e3 ubiquitin ligase bound to compound furan 24 (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 15 (66 kDa, Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- 5-[[3,4-bis(chloranyl)-1~{h}-indol-7-yl]sulfamoyl]-~{n},~{n},3-trimethyl-furan-2-carboxamide;ethane (416 Da, Ligand)
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8roy
Q-score: 0.477
Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnstrom M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI
J Med Chem (2024) 67 pp. 5538-5566 [ Pubmed: 38513086 DOI: doi:10.1021/acs.jmedchem.3c02136 ]
- Complex of the human ddb1-dda1-dcaf15 e3 ubiquitin ligase bound to compound furan 24 (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 15 (66 kDa, Protein from Homo sapiens)
- Det1- and ddb1-associated protein 1 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (93 kDa, Protein from Homo sapiens)
- 1-[5-[[3,4-bis(chloranyl)-1~{h}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{n}-methyl-piperidine-4-carboxamide (513 Da, Ligand)
Eaf3 CHD domain bound to the nucleosome
Resolution: 3.58 Å
EM Method: Single-particle
Fitted PDBs: 8ihm
Q-score: 0.434
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Histone h4 (11 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 (13 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Rco1-abr (2 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the Rpd3S core complex
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 8ihn
Q-score: 0.48
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Histone h3 (2 kDa, Protein from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8iht
Q-score: 0.345
Zhang Y, Xu M, Wang P, Zhou J, Wang G, Han S, Cai G, Wang X
Cell Res (2023) 33 pp. 971-974 [ DOI: doi:10.1038/s41422-023-00884-2 Pubmed: 37845487 ]
- Dna (165-mer) (51 kDa, DNA from Xenopus laevis)
- Rco1 isoform 1 (78 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Transcriptional regulatory protein sin3 (175 kDa, Protein from Saccharomyces cerevisiae)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Eaf3 chd domain bound to the nucleosome (Complex from Xenopus laevis)
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae)
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae)
- Calcium ion (40 Da, Ligand)
- Dna (164-mer) (50 kDa, DNA from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
XBB.1.5.10 RBD in complex with ACE2
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8wtd
Q-score: 0.508
Jian F, Feng L, Yang S, Yu Y, Wang L, Song W, Yisimayi A, Chen X, Xu Y, Wang P, Yu L, Wang J, Liu L, Niu X, Wang J, Xiao T, An R, Wang Y, Gu Q, Shao F, Jin R, Shen Z, Wang Y, Wang X, Cao Y
PLoS Pathog (2023) 19 pp. e1011868-e1011868 [ Pubmed: 38117863 DOI: doi:10.1371/journal.ppat.1011868 ]
- Rbd in complex with ace2 (Complex)
- Human ace2 (Complex from Homo sapiens)
- Spike protein s2' (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Xbb.1.5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (92 kDa, Protein from Homo sapiens)
XBB.1.5.70 spike protein in complex with ACE2
Resolution: 4.64 Å
EM Method: Single-particle
Fitted PDBs: 8wtj
Q-score: 0.202
Jian F, Feng L, Yang S, Yu Y, Wang L, Song W, Yisimayi A, Chen X, Xu Y, Wang P, Yu L, Wang J, Liu L, Niu X, Wang J, Xiao T, An R, Wang Y, Gu Q, Shao F, Jin R, Shen Z, Wang Y, Wang X, Cao Y
PLoS Pathog (2023) 19 pp. e1011868-e1011868 [ Pubmed: 38117863 DOI: doi:10.1371/journal.ppat.1011868 ]
- Spike glycoprotein (145 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Human ace2 (Complex from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (68 kDa, Protein from Homo sapiens)
- Xbb.1.5.70 spike protein in complex with hace2 (Complex)