The ternary complex of DDB1, DDA1, DET1
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9dhd
Q-score: 0.517
Karayel O, Soung A, Gurung H, Schubert AF, Kschonsak M, Dugger DL, Webster JD, French DM, Klaeger S, Rose CM, Harris SF, Ndoja A, Newton K, Dixit VM
To Be Published
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Det1 homolog (64 kDa, Protein from Homo sapiens)
- Ddb1:dda1:det1 (205 kDa, Complex from Homo sapiens)
- Det1- and ddb1-associated protein 1 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of DDB1deltaB-DDA1-DCAF5
Resolution: 2.63 Å
EM Method: Single-particle
Fitted PDBs: 8tl6
Q-score: 0.598
Radko-Juettner S, Yue H, Myers JA, Carter RD, Robertson AN, Mittal P, Zhu Z, Hansen BS, Donovan KA, Hunkeler M, Rosikiewicz W, Wu Z, McReynolds MG, Roy Burman SS, Schmoker AM, Mageed N, Brown SA, Mobley RJ, Partridge JF, Stewart EA, Pruett-Miller SM, Nabet B, Peng J, Gray NS, Fischer ES, Roberts CWM
Nature (2024) 628 pp. 442-449 [ Pubmed: 38538798 DOI: doi:10.1038/s41586-024-07250-1 ]
- Det1- and ddb1-associated protein 1 (14 kDa, Protein from Homo sapiens)
- Complex of ddb1deltab-dda1-dcaf5 (220 kDa, Complex from Homo sapiens)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 5 (108 kDa, Protein from Homo sapiens)
Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1
Resolution: 2.41 Å
EM Method: Single-particle
Fitted PDBs: 8tnq
Q-score: 0.591
Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR
Science (2024) 383 pp. eadk4422-eadk4422 [ DOI: doi:10.1126/science.adk4422 Pubmed: 38484051 ]
- Protein cereblon (55 kDa, Protein from Homo sapiens)
- 2-[(3s)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1h-isoindole-1,3(2h)-dione (343 Da, Ligand)
- Ternary complex of ddb1db:crbn:pt-179 with sd40 (201 kDa, Complex)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Maltose/maltodextrin-binding periplasmic protein,sd40 (50 kDa, Protein from Homo sapiens)
Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8tnr
Q-score: 0.561
Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR
Science (2024) 383 pp. eadk4422-eadk4422 [ Pubmed: 38484051 DOI: doi:10.1126/science.adk4422 ]
- Ternary complex of ddb1db:crbn:pt-179 with sd40 (201 kDa, Complex)
- 2-[(3s)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1h-isoindole-1,3(2h)-dione (343 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Maltose/maltodextrin-binding periplasmic protein,sd40 (50 kDa, Protein from Homo sapiens)
- Protein cereblon (55 kDa, Protein from Homo sapiens)
Map from local refinement (focused on CRBN) of DDB1dB:CRBN:PT-179:SD40, conformation 1
Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR
Science (2024) 383 pp. eadk4422-eadk4422 [ DOI: doi:10.1126/science.adk4422 Pubmed: 38484051 ]
Map from local refinement (focused on CRBN) of DDB1dB:CRBN:PT-179:SD40, conformation 2
Mercer JAM, DeCarlo SJ, Roy Burman SS, Sreekanth V, Nelson AT, Hunkeler M, Chen PJ, Donovan KA, Kokkonda P, Tiwari PK, Shoba VM, Deb A, Choudhary A, Fischer ES, Liu DR
Science (2024) 383 pp. eadk4422-eadk4422 [ DOI: doi:10.1126/science.adk4422 Pubmed: 38484051 ]
Structure of the Pol II-TCR-ELOF1 complex.
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b3d
Q-score: 0.532
To Be Published
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Transcription elongation factor 1 homolog (9 kDa, Protein from Homo sapiens)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase subunit (217 kDa, Protein from Sus scrofa domesticus)
- Rna (3 kDa, RNA from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa domesticus)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase subunit beta (133 kDa, Protein from Sus scrofa domesticus)
- Nts (16 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa domesticus)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna polymerase ii subunit d (16 kDa, Protein from Sus scrofa domesticus)
- Uv-stimulated scaffold protein a (80 kDa, Protein from Homo sapiens)
- Pol ii-tcr-elof1 complex. (Complex from Homo sapiens)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa domesticus)
- Ts (15 kDa, DNA from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Rpb7 (28 kDa, Protein from Sus scrofa domesticus)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa domesticus)
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)
- Ddb1- and cul4-associated factor 16 (24 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)
- Bromodomain-containing protein 4 (14 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)
- Det1- and ddb1-associated protein 1 (12 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (96 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5
Resolution: 2.83 Å
EM Method: Single-particle
Fitted PDBs: 8ajm
Q-score: 0.425
Pla-Prats C, Cavadini S, Kempf G, Thoma NH
EMBO J (2023) 42 pp. e112253-e112253 [ DOI: doi:10.15252/embj.2022112253 Pubmed: 36715408 ]
- T-complex protein 1 subunit epsilon (62 kDa, Protein from Homo sapiens)
- Complex of ddb1-dcaf12-cct5 (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Ddb1- and cul4-associated factor 12 (53 kDa, Protein from Homo sapiens)
Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 7oob
Q-score: 0.566
Kokic G, Wagner FR, Chernev A, Urlaub H, Cramer P
Nature (2021) 598 pp. 368-372 [ DOI: doi:10.1038/s41586-021-03906-4 Pubmed: 34526721 ]
- Nts (14 kDa, DNA from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc3 (17 kDa, Protein from Sus scrofa)
- Rpol4c domain-containing protein (16 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb9 (14 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb3 (31 kDa, Protein from Sus scrofa)
- Ts (14 kDa, DNA from Homo sapiens)
- Nts, rna, ts (Complex from Homo sapiens)
- Dna-directed rna polymerase subunit beta (134 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit f (14 kDa, Protein from Sus scrofa)
- Dna excision repair protein ercc-6 (168 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerase with rna_pol_l_2 and rna polymerase (Complex from Sus scrofa)
- Dna-directed rna polymerase ii subunit e (24 kDa, Protein from Sus scrofa)
- Beryllium trifluoride ion (66 Da, Ligand)
- Dna-directed rna polymerase ii subunit rpb7 (19 kDa, Protein from Sus scrofa)
- Dna-directed rna polymerase ii subunit rpb1 (217 kDa, Protein from Sus scrofa)
- Rna (3 kDa, RNA from Homo sapiens)
- Rna_pol_l_2 domain-containing protein (13 kDa, Protein from Sus scrofa)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Rna polymerase ii subunit k (7 kDa, Protein from Sus scrofa)
- Zinc ion (65 Da, Ligand)
- Complex between the transcribing rna polymerase ii and tcr factors in the presence of adp-bef3. (Complex)
- Magnesium ion (24 Da, Ligand)
- Dna excision repair protein ercc-6 and ercc-8, dna damage-binding protein 1 (Complex from Homo sapiens)
- Dna excision repair protein ercc-8 (44 kDa, Protein from Homo sapiens)
- Dna-directed rna polymerases i, ii, and iii subunit rpabc5 (7 kDa, Protein from Sus scrofa)