Do data resources managed by EMBL-EBI and our collaborators make a difference to your work? Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research. We appreciate your responses prior to closing of the survey on Monday 17th June.
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 ]
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 h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
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 ]
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 ]
- Histone h3.1 (15 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)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein 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)
- Nucleosomal core particle (Complex)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex 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)
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 from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Nucleosomal core particle (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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
- Oct4-gfp (Protein from Homo sapiens)
- Histone h4 (Protein from Homo sapiens)
- Oct4-gfp (Complex from Homo sapiens)
- Histones, human_cmyc and human_max (Complex from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Histone h2b type 1-j (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Histone h3.1 (Protein from Homo sapiens)
- Human_max (Protein from Homo sapiens)
- 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 ]
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosome core particle (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 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)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
- Histone octamer (Complex from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
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 [ Pubmed: 37407816 DOI: doi:10.1038/s41586-023-06282-3 ]
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)
- Histone h4 (Protein from Homo sapiens)
- Dna (Complex from Synthetic construct)
- Max (Complex from Homo sapiens)
- Histone h2b type 1-j (Protein from Homo sapiens)
- Histone h2a type 1-b/e (Protein from Homo sapiens)
- Dna (127-mer) (DNA from synthetic construct)
- Histone h3.1 (Protein from Homo sapiens)
- Max (Protein from Homo sapiens)
- Histones (Complex 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 ]
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (59 kDa, Protein from Homo sapiens)
- Nucleosome-bound factors (Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Nucleosomal dna (Complex from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Myc-max and oct4-bound nucleosome (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Nucleosomal core particle (Complex)
- Histone octamer (Complex from Homo sapiens)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Protein max (9 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Oct4 (Complex from Homo sapiens)