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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Nucleosome core particle (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
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)
- Dna (124-mer) (47 kDa, DNA from synthetic construct)
- Nucleosomal core particle (Complex)
- Histone h2b type 1-j (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 dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Dna (124-mer) (46 kDa, DNA from synthetic construct)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Circadian locomoter output cycles protein kaput (43 kDa, Protein from Mus musculus)
- Clock-bmal1 bound to a nucleosome at shl -6.2 (Complex)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Basic helix-loop-helix arnt-like protein 1 (43 kDa, Protein from Mus musculus)
- Nucleosome core particle (Complex)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Clock-bmal1 heterodimer (Complex from Mus musculus)
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 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Myc proto-oncogene protein (11 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Nucleosome-bound factors (Complex)
- Nucleosomal core particle (Complex)
- Myc-max and oct4-bound nucleosome (Complex)
- Cmyc-max heterodimer (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Protein max (9 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)
- Nucleosomal dna (Complex from synthetic construct)
- Histone octamer (Complex from Homo sapiens)
- Oct4 (Complex from Homo sapiens)
- Dna (127-mer) (39 kDa, DNA from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Structure of human cGAS (K394E) bound to the nucleosome
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6y5d
Q-score: 0.195
Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A
Nature (2020) 587 pp. 668-672 [ Pubmed: 32911482 DOI: doi:10.1038/s41586-020-2750-6 ]
- Histone h2a type 2-a (14 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-a (Complex from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Histone h2b type 1-k (13 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Cryo-em structure of cgas-ncp complex (240 kDa, Complex)
Structure of human cGAS (K394E) bound to the nucleosome (focused refinement of cGAS-NCP subcomplex)
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 6y5e
Q-score: 0.43
Pathare GR, Decout A, Gluck S, Cavadini S, Makasheva K, Hovius R, Kempf G, Weiss J, Kozicka Z, Guey B, Melenec P, Fierz B, Thoma NH, Ablasser A
Nature (2020) 587 pp. 668-672 [ Pubmed: 32911482 DOI: doi:10.1038/s41586-020-2750-6 ]
- Pentanedial (100 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Histone h4 (Complex from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from Homo sapiens)
- Histone h3.2 (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Histone h2a type 2-c (11 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from Homo sapiens)
- Protein (Complex from Homo sapiens)
- Cyclic gmp-amp synthase (42 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Cryo em structure of cgas-ncp1 complex (240 kDa, Complex)
- Histone h4 (9 kDa, Protein from Homo sapiens)
OCT4-SOX2-bound nucleosome - SHL-6
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 6t90
Q-score: 0.451
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH
Science (2020) 368 pp. 1460-1465 [ Pubmed: 32327602 DOI: doi:10.1126/science.abb0074 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (146-mer) (46 kDa, DNA from synthetic construct)
- Pentanedial (100 Da, Ligand)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (70 kDa, Protein from Homo sapiens)
- G protein/gfp fusion protein,pou domain, class 5, transcription factor 1 (oct4) (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Sox2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Ternary complex of oct4-sox2 and shl-6 nucleosome (Complex)
Nucleosome with OCT4-SOX2 motif at SHL-6
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 6t93
Q-score: 0.419
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH
Science (2020) 368 pp. 1460-1465 [ Pubmed: 32327602 DOI: doi:10.1126/science.abb0074 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
- Histones (Complex from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
OCT4-SOX2-bound nucleosome - SHL+6
Resolution: 3.42 Å
EM Method: Single-particle
Fitted PDBs: 6yov
Q-score: 0.35
Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schubeler D, Thoma NH
Science (2020) 368 pp. 1460-1465 [ Pubmed: 32327602 DOI: doi:10.1126/science.abb0074 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Dna (142-mer) (92 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Sox2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (69 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)