Cryo-EM structure of the ZBTB5 BTB domain filament
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 9b9r
Q-score: 0.315
Park PMC, Park J, Brown J, Hunkeler M, Roy Burman SS, Donovan KA, Yoon H, Nowak RP, Slabicki M, Ebert BL, Fischer ES
Mol Cell (2024) 84 pp. 2511-2524.e8 [ Pubmed: 38996460 DOI: doi:10.1016/j.molcel.2024.06.010 ]
Cryo-EM structure of the ZBTB9 BTB domain filament
Resolution: 8.1 Å
EM Method: Helical reconstruction
Fitted PDBs: 9b9v
Q-score: 0.168
Park PMC, Park J, Brown J, Hunkeler M, Roy Burman SS, Donovan KA, Yoon H, Nowak RP, Slabicki M, Ebert BL, Fischer ES
Mol Cell (2024) 84 pp. 2511-2524.e8 [ Pubmed: 38996460 DOI: doi:10.1016/j.molcel.2024.06.010 ]
Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8g46
Q-score: 0.643
Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Lumpkin R, Sandoval B, Jin CY, Ficarro SB, Wang MY, Xu S, Groendyke BJ, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Marto JA, Qi J, Nowak RP, Donovan KA, Slabicki M, Gray NS, Fischer ES, Ebert BL
bioRxiv (2023) [ DOI: doi:10.1101/2023.02.14.528208 Pubmed: 36824856 ]
- Water (18 Da, Ligand)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Tert-butyl [(6s,10p)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6h-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate (529 Da, Ligand)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Bromodomain-containing protein 4 (14 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ddb1- and cul4-associated factor 16 (24 kDa, Protein from Homo sapiens)
- Ternary complex of cullin ring e3 ubiquitin ligase substrate receptor arm (ddb1deltab-dda1-dcaf16) in compound-induced complex with bromodomain 2 of brd4 (148 kDa, Complex from Homo sapiens)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8e4y
Q-score: 0.502
Johnson ZL, Ammirati M, Wasilko DJ, Chang JS, Noell S, Foley TL, Yoon H, Smith K, Asano S, Hales K, Wan M, Yang Q, Piotrowski MA, Farley KA, Gilbert T, Aschenbrenner LM, Fennell KF, Dutra JK, Xu M, Guo C, Varghese AE, Bellenger J, Quinn A, Am Ende CW, West GM, Griffor MC, Bennett D, Calabrese M, Steppan CM, Han S, Wu H
Nat Struct Mol Biol (2023) 30 pp. 22-30 [ Pubmed: 36522428 DOI: doi:10.1038/s41594-022-00884-7 ]
- [(2r,3s,4r,5r)-5-(6-amino-9h-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl (3r)-3-hydroxy-2,2-dimethyl-4-oxo-4-{[3-oxo-3-({2-[(2-oxohexadecyl)sulfanyl]ethyl}amino)propyl]amino}butyl dihydrogen diphosphate (non-preferred name) (1 kDa, Ligand)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate (410 Da, Ligand)
- Glycerol-3-phosphate acyltransferase 1, mitochondrial (86 kDa, Protein from Homo sapiens)
- Glycerol-3-phosphate acyltransferase 1 (86 kDa, Complex from Homo sapiens)
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8e50
Q-score: 0.444
Johnson ZL, Ammirati M, Wasilko DJ, Chang JS, Noell S, Foley TL, Yoon H, Smith K, Asano S, Hales K, Wan M, Yang Q, Piotrowski MA, Farley KA, Gilbert T, Aschenbrenner LM, Fennell KF, Dutra JK, Xu M, Guo C, Varghese AE, Bellenger J, Quinn A, Am Ende CW, West GM, Griffor MC, Bennett D, Calabrese M, Steppan CM, Han S, Wu H
Nat Struct Mol Biol (2023) 30 pp. 22-30 [ Pubmed: 36522428 DOI: doi:10.1038/s41594-022-00884-7 ]
- Coenzyme a (767 Da, Ligand)
- (2r)-2-hydroxy-3-(phosphonooxy)propyl hexadecanoate (410 Da, Ligand)
- Glycerol-3-phosphate acyltransferase 1, mitochondrial (86 kDa, Protein from Homo sapiens)
- Glycerol-3-phosphate acyltransferase 1 (86 kDa, Complex from Homo sapiens)
Cryo-EM structure of BCL6 bound to BI-3802
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6xmx
Q-score: 0.285
Slabicki M, Yoon H, Koeppel J, Nitsch L, Roy Burman SS, Di Genua C, Donovan KA, Sperling AS, Hunkeler M, Tsai JM, Sharma R, Guirguis A, Zou C, Chudasama P, Gasser JA, Miller PG, Scholl C, Frohling S, Nowak RP, Fischer ES, Ebert BL
Nature (2020) 588 pp. 164-168 [ Pubmed: 33208943 DOI: doi:10.1038/s41586-020-2925-1 ]
- B-cell lymphoma 6 protein (bcl6) filament (352 kDa, Cellular component from Homo sapiens)
- B-cell lymphoma 6 protein (44 kDa, Protein from Homo sapiens)
- 2-[6-[[5-chloranyl-2-[(3~{s},5~{r})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{n}-methyl-ethanamide (484 Da, Ligand)
Cryo-EM structure of DDB1dB-DCAF15-DDA1 bound to E7820 and RBM39
Faust TB, Yoon H, Nowak RP, Donovan KA, Li Z, Cai Q, Eleuteri NA, Zhang T, Gray NS, Fischer ES
Nat Chem Biol (2020) 16 pp. 7-14 [ DOI: doi:10.1038/s41589-019-0378-3 Pubmed: 31686031 ]
- Ddb1 and cul4 associated factor 15 (Protein from Homo sapiens)
- Dna damage-binding protein 1 (Protein from Homo sapiens)
- Det1 and ddb1 associated 1 (Protein from Homo sapiens)
- Rna binding motif protein 39 (Protein from Homo sapiens)
- Complex of ddb1-dcaf15-dda1 bound to e7820 and the second rrm of rbm39 (193 kDa, Complex from Homo sapiens)
Cryo-EM structure of DDB1-DCAF15 bound to E7820 and the second RRM of RBM39
Faust TB, Yoon H, Nowak RP, Donovan KA, Li Z, Cai Q, Eleuteri NA, Zhang T, Gray NS, Fischer ES
Nat Chem Biol (2020) 16 pp. 7-14 [ DOI: doi:10.1038/s41589-019-0378-3 Pubmed: 31686031 ]