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)
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 [ DOI: doi:10.1126/science.abb0074 Pubmed: 32327602 ]
- Histones (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Ternary complex of oct4-sox2 and shl-6 nucleosome (Complex)
- Sox2 (Complex from Homo sapiens)
- Dna (146-mer) (46 kDa, DNA from synthetic construct)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (70 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- G protein/gfp fusion protein,pou domain, class 5, transcription factor 1 (oct4) (Complex from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1126/science.abb0074 Pubmed: 32327602 ]
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Dna (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
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 [ DOI: doi:10.1126/science.abb0074 Pubmed: 32327602 ]
- Histones (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Sox2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (Complex from Homo sapiens)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Dna (142-mer) (92 kDa, DNA from synthetic construct)
- Dna (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein 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 (69 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 6r8y
Q-score: 0.313
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Dna damage-binding proteins (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (44 kDa, DNA from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a 6-4pp containing nucleosome (199 kDa, Complex)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP_THF2(-1)-UV-DDB
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6r8z
Q-score: 0.307
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome (199 kDa, Complex)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A
Resolution: 4.5 Å
EM Method: Single-particle
Fitted PDBs: 6r90
Q-score: 0.278
Matsumoto S, Cavadini S, Bunker RD, Grand RS, Potenza A, Rabl J, Yamamoto J, Schenk AD, Schubeler D, Iwai S, Sugasawa K, Kurumizaka H, Thoma NH
Nature (2019) 571 pp. 79-84 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome class a (199 kDa, Complex)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)