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 ]
- Sox2 (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (146-mer) (46 kDa, DNA from synthetic construct)
- Ternary complex of oct4-sox2 and shl-6 nucleosome (Complex)
- 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)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (70 kDa, Protein from Homo sapiens)
- Dna (146-mer) (45 kDa, DNA from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Histones (Complex 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 (Complex from synthetic construct)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna (153-mer) (46 kDa, DNA from synthetic construct)
- Dna (153-mer) (47 kDa, DNA from synthetic construct)
- Histones (Complex from Homo sapiens)
- Histone h4 (11 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)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Transcription factor sox-2 (12 kDa, Protein from Homo sapiens)
- Pentanedial (100 Da, Ligand)
- Ternary complex of oct4-sox2 and shl+6 nucleosome (Complex)
- Dna (142-mer) (92 kDa, DNA from synthetic construct)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Sox2 (Complex from Homo sapiens)
- Dna (Complex from synthetic construct)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histones (Complex from Homo sapiens)
- Green fluorescent protein,pou domain, class 5, transcription factor 1 (69 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein 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)
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 ]
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (44 kDa, DNA from Homo sapiens)
- Dna damage-binding proteins (Complex from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 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 h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1 (127 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histones (Complex 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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Uv-ddb bound to a thf2 containing nucleosome (199 kDa, Complex)
- Dna (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 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 h4 (11 kDa, Protein from Homo sapiens)
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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Dna (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome class a (199 kDa, Complex)
Cryo-EM structure of NCP_THF2(-3)-UV-DDB
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 6r91
Q-score: 0.212
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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Dna (Complex from Homo sapiens)
- Dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Uv-ddb bound to a thf2 (-3) containing nucleosome (Complex)
Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 6r92
Q-score: 0.22
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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Dna (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 (+1) containing nucleosome class b (Complex)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Dna damage-binding protein 1,dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
Cryo-EM structure of NCP-6-4PP
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 6r93
Q-score: 0.352
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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Dna (Complex from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (45 kDa, DNA from Homo sapiens)
- 6-4pp nucleosome (199 kDa, Complex)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (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) (44 kDa, DNA from Homo sapiens)
Cryo-EM structure of NCP_THF2(-3)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6r94
Q-score: 0.363
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 [ Pubmed: 31142837 DOI: doi:10.1038/s41586-019-1259-3 ]
- Human dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Thf2 (-3) containing nucleosome (199 kDa, Complex)
- Histone h3.1 / 2a / 2b (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)