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 ]
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)
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 ]
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)
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 octamer (Complex from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Nucleosomal dna (Complex from synthetic construct)
- Nucleosomal core particle (Complex from Homo sapiens)
- Clock-bmal1 bound to a nucleosome shl+5.8 (Complex from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Oct4-gfp (Complex from Homo sapiens)
- Human_max (Protein from Homo sapiens)
- Histones, human_cmyc and human_max (Complex from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Human_cmyc (Protein from Homo sapiens)
- Oct4-gfp (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Histone h3.1 (Protein from Homo sapiens)
- Histone h2b type 1-j (Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
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)
Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 1)
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 ]
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 [ DOI: doi:10.1038/s41586-023-06282-3 Pubmed: 37407816 ]
- Histones (Complex from Homo sapiens)
- Dna (127-mer) (DNA from synthetic construct)
- Max-max bound to a nucleosome at shl+5.1 and shl-6.9 (Complex)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Max (Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Max (Complex from Homo sapiens)
- Histone h3.1 (Protein from Homo sapiens)
- 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 [ 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)