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)
Cryo-EM structure of the BRISC complex bound to SHMT2
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 6h3c
Q-score: 0.278
Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andres-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guerillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thoma NH
Mol Cell (2019) 75 pp. 483-497.e9 [ DOI: doi:10.1016/j.molcel.2019.06.002 Pubmed: 31253574 ]
- Shmt2 alpha (Complex from Homo sapiens)
- Lys-63-specific deubiquitinase brcc36 (38 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Brisc complex subunit abraxas 2 (49 kDa, Protein from Homo sapiens)
- Brisc and brca1-a complex member 2 (45 kDa, Protein from Homo sapiens)
- Brisc and brca1-a complex member 1 (39 kDa, Protein from Homo sapiens)
- Brisc complex bound to shmt2 alpha (438 kDa, Complex)
- Serine hydroxymethyltransferase, mitochondrial (56 kDa, Protein from Homo sapiens)
- Brisc complex (Complex from Homo sapiens)
- Water (18 Da, Ligand)
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 protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein 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)
- Histones (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with a 6-4pp at positions 95-96 (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Dna damage-binding proteins (Complex from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA 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 ]
- Dna damage-binding protein 2 (48 kDa, Protein from Homo sapiens)
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome (199 kDa, Complex)
- Dna damage-binding protein 1 (129 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) (44 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Uv-ddb bound to a thf2 containing nucleosome class a (199 kDa, Complex)
- Histone h3.1, histone h2a, histone h2b (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)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex 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)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 97-98 (44 kDa, DNA from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (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)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex 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)
- Dna (Complex from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 (-3) containing nucleosome (Complex)
- Histone h2b type 1-j (14 kDa, Protein from Homo sapiens)
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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (11 kDa, Protein from Homo sapiens)
- Histone h4 (Complex from Homo sapiens)
- Histone h3.1, histone h2a, histone h2b (Complex from Homo sapiens)
- Dna damage-binding protein 1,dna damage-binding protein 1 (129 kDa, Protein from Homo sapiens)
- Uv-ddb bound to a thf2 (+1) containing nucleosome class b (Complex)
- Dna damage-binding protein 1(2), dna damage-binding protein 2 (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) (44 kDa, DNA from Homo sapiens)
- Dna damage-binding protein 2 (50 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- Dna (Complex from Homo sapiens)
- Human alpha-satellite dna (145-mer) with abasic sites at positions 93-94 (44 kDa, DNA from Homo sapiens)
- Histone h2b type 1-j (14 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 [ DOI: doi:10.1038/s41586-019-1259-3 Pubmed: 31142837 ]
- Histone h3.1 (15 kDa, Protein from Homo sapiens)
- Histone h4 (Complex 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)
- Histone h2a type 1-b/e (14 kDa, Protein from Homo sapiens)
- 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 h2b type 1-j (14 kDa, Protein from Homo sapiens)
- 6-4pp nucleosome (199 kDa, Complex)