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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- [ DOI: doi:10.1016/j.molcel.2023.06.028 Pubmed: 37478846 ]
- Tetramer of ubr5 (Complex from Homo sapiens)
- E3 ubiquitin-protein ligase ubr5 (313 kDa, Protein from Homo sapiens)
Negative stain map of UBR5 (dimer) in complex with RARA/RXRA
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 [ DOI: doi:10.1016/j.molcel.2023.06.028 Pubmed: 37478846 ]
- Rara (Protein from Homo sapiens)
- Ubr5 (Protein from Homo sapiens)
- Rxra (Protein from Homo sapiens)
- Ubr5 in complex with rara/rxra (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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Nucleosome core particle (Complex)
- 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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Nucleosomal core particle (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (124-mer) (46 kDa, DNA from synthetic construct)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
Cryo-EM map of MYC-MAX-OCT4-LIN28 complex
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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Histones, human_cmyc and human_max (Complex from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Oct4-gfp (Complex from Homo sapiens)
- Histone h3.1 (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Human_max (Protein from Homo sapiens)
- Oct4-gfp (Protein from Homo sapiens)
- Histone h2b type 1-j (Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Human_cmyc (Protein from Homo sapiens)
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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Histone h2a type 1-b/e (14 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 octamer (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Nucleosome core particle (Complex)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
MAX-MAX bound to a nucleosome at SHL+5.1 and SHL-6.9.
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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Max-max bound to a nucleosome at shl+5.1 and shl-6.9 (Complex)
- Histones (Complex from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Dna (127-mer) (DNA from synthetic construct)
- Max (Protein from Homo sapiens)
- Histone h3.1 (Protein from Homo sapiens)
- Max (Complex from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Histone h2b type 1-j (Protein 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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Pentanedial (100 Da, Ligand)
- Nucleosomal core particle (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Nucleosome-bound factors (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Oct4 (Complex from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Protein max (9 kDa, Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
MYC-MAX bound to a nucleosome at SHL+5.8
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8ott
Q-score: 0.411
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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Pentanedial (100 Da, Ligand)
- Myc-max bound to a nucleosome at shl+5.8 (Complex)
- Nucleosomal core particle (Complex)
- Myc proto-oncogene protein (6 kDa, Protein from Homo sapiens)
- Protein max (6 kDa, Protein from Homo sapiens)
- Histone h2a type 1-k (11 kDa, Protein from Homo sapiens)
- Histone octamer (Complex from Homo sapiens)
- Histone h2b type 1-j (10 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Cmyc/max heterodimer (Complex from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Dna (144-mer) (44 kDa, DNA from synthetic construct)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
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)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Complex of ddb1-dcaf12-cct5 (Complex from Homo sapiens)
- Ddb1- and cul4-associated factor 12 (53 kDa, Protein from Homo sapiens)