Monomeric E6AP-E6-p53 ternary complex
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 8r1f
Q-score: 0.316
Sandate CR, Chakraborty D, Kater L, Kempf G, Thoma NH
bioRxiv (2023) [ DOI: doi:10.1101/2023.11.01.565136 ]
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Zinc ion (65 Da, Ligand)
- Monomeric e6ap-e6-p53 ternary complex (176 kDa, Complex from Homo sapiens)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
Dimeric ternary structure of E6AP-E6-p53
Resolution: 3.99 Å
EM Method: Single-particle
Fitted PDBs: 8r1g
Q-score: 0.175
Sandate CR, Chakraborty D, Kater L, Kempf G, Thoma NH
bioRxiv (2023) [ DOI: doi:10.1101/2023.11.01.565136 ]
- Cellular tumor antigen p53 (46 kDa, Protein from Homo sapiens)
- Dimeric e6ap-e6-p53 ternary complex (352 kDa, Complex from Homo sapiens)
- Ubiquitin-like protein smt3,protein e6 (31 kDa, Protein from Human papillomavirus type 16)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-protein ligase e3a (103 kDa, Protein from Homo sapiens)
Cryo-EM structure of dimeric UBR5
Resolution: 3.36 Å
EM Method: Single-particle
Fitted PDBs: 8p82
Q-score: 0.299
Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Slabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thoma NH, Ebert BL
Mol Cell (2023) 83 pp. 2753-2767.e10 [ Pubmed: 37478846 DOI: doi:10.1016/j.molcel.2023.06.028 ]
- E3 ubiquitin-protein ligase ubr5 (313 kDa, Protein from Homo sapiens)
- Dimer of ubr5 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of full-length human UBR5 (homotetramer)
Resolution: 3.87 Å
EM Method: Single-particle
Fitted PDBs: 8p83
Q-score: 0.2
Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Slabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thoma NH, Ebert BL
Mol Cell (2023) 83 pp. 2753- [ Pubmed: 37478846 DOI: doi:10.1016/j.molcel.2023.06.028 ]
- E3 ubiquitin-protein ligase ubr5 (313 kDa, Protein from Homo sapiens)
- Tetramer of ubr5 (Complex from Homo sapiens)
Resolution: 6.2 Å
EM Method: Single-particle
Fitted PDBs: 8osj
Q-score: 0.219
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH
Nature (2023) 619 pp. 385-393 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Nucleosome core particle (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 8osk
Q-score: 0.267
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH
Nature (2023) 619 pp. 385-393 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Dna (124-mer) (46 kDa, DNA from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Nucleosomal core particle (Complex)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
Resolution: 4.9 Å
EM Method: Single-particle
Fitted PDBs: 8osl
Q-score: 0.177
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH
Nature (2023) 619 pp. 385-393 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Nucleosome core particle (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
OCT4 and MYC-MAX co-bound to a nucleosome
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ots
Q-score: 0.404
Michael AK, Stoos L, Crosby P, Eggers N, Nie XY, Makasheva K, Minnich M, Healy KL, Weiss J, Kempf G, Cavadini S, Kater L, Seebacher J, Vecchia L, Chakraborty D, Isbel L, Grand RS, Andersch F, Fribourgh JL, Schubeler D, Zuber J, Liu AC, Becker PB, Fierz B, Partch CL, Menet JS, Thoma NH
Nature (2023) 619 pp. 385-393 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome-bound factors (Complex)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Oct4 (Complex from Homo sapiens)
- Protein max (9 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Nucleosomal core particle (Complex)
- Myc-max and oct4-bound nucleosome (Complex)
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 ]
- Complex of ddb1-dcaf12-cct5 (Complex from Homo sapiens)
- T-complex protein 1 subunit epsilon (62 kDa, Protein 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)
Structure of the human DDB1-DCAF12 complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ajn
Q-score: 0.27
Pla-Prats C, Cavadini S, Kempf G, Thoma NH
EMBO J (2023) 42 pp. e112253-e112253 [ DOI: doi:10.15252/embj.2022112253 Pubmed: 36715408 ]
- Complex of ddb1-dcaf12 (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)