Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of nucleosome)
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8g86
Q-score: 0.606
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ Pubmed: 37225990 DOI: doi:10.1038/s41586-023-06112-6 ]
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Nmatn1 dna (top stand) (56 kDa, DNA from Homo sapiens)
- Histone h4 (11 kDa, Protein from Xenopus laevis laevis)
- Nmatn1 dna (bottom strand) (57 kDa, DNA from Homo sapiens)
- Nucleosome with human nmatn1 sequence (Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Human Oct4 bound to nucleosome with human nMatn1 sequence (focused refinement of Oct4 bound region)
Resolution: 8.1 Å
EM Method: Single-particle
Fitted PDBs: 8g87
Q-score: 0.064
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
- Nmatn1 dna (top strand) (56 kDa, DNA from Homo sapiens)
- Nucleosome with human nmatn1 sequence (Complex from Xenopus laevis)
- Pou domain, class 5, transcription factor 1 (42 kDa, Protein from Homo sapiens)
- Nmatn1 dna (bottom strand) (57 kDa, DNA from Homo sapiens)
Human Oct4 bound to nucleosome with human nMatn1 sequence
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8g88
Q-score: 0.199
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ Pubmed: 37225990 DOI: doi:10.1038/s41586-023-06112-6 ]
- Nmatn1 dna top strand (168-mer) (56 kDa, DNA from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Nmatn1 dna bottom strand (168-mer) (57 kDa, DNA from Homo sapiens)
- Pou domain, class 5, transcription factor 1 (42 kDa, Protein from Homo sapiens)
- Nucleosome with human nmatn1 sequence (Complex from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
Nucleosome with human nMatn1 sequence in complex with Human Oct4
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8g8b
Q-score: 0.233
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
- Nmatn1 dna (top strand,168-mer) (56 kDa, DNA from Homo sapiens)
- Nmatn1 dna (bottom strand, 168-mer) (57 kDa, DNA from Homo sapiens)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Human oct4 bound to nucleosome with human nmatn1 sequence (Complex from Xenopus laevis)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pou domain, class 5, transcription factor 1 (42 kDa, Protein from Homo sapiens)
Human Oct4 bound to nucleosome with human LIN28B sequence
Resolution: 3.9 Å
EM Method: Single-particle
Fitted PDBs: 8g8e
Q-score: 0.254
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
- Lin28b dna (32-mer) (55 kDa, DNA from Homo sapiens)
- Lin28b dna (32-mer) (56 kDa, DNA from Homo sapiens)
- Pou domain, class 5, transcription factor 1 (42 kDa, Protein from Homo sapiens)
- Human oct4 bound to a nucleosome with human lin28 dna sequence (Complex from Homo sapiens)
Interaction of H3 tail in LIN28B nucleosome with Oct4
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8g8g
Q-score: 0.218
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
- Nucleosome with human lin28b sequence bound to human oct4 (Complex from Xenopus laevis)
- Histone h2a (13 kDa, Protein from Xenopus laevis)
- Histone h2b (13 kDa, Protein from Xenopus laevis)
- Histone h4 (11 kDa, Protein from Xenopus laevis)
- Lin28b dna (174-mer) (56 kDa, DNA from Homo sapiens)
- Lin28b dna (174-mer) (55 kDa, DNA from Homo sapiens)
- Histone h3 (15 kDa, Protein from Xenopus laevis)
- Pou domain, class 5, transcription factor 1 (42 kDa, Protein from Homo sapiens)
Oct4 interaction with H2A C-terminal tail in LIN28B nucleosome
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
H4 tail conformation A in Oct4 bound LIN28 nucleosome
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
H4 tail conformation B in Oct4 bound LIN28B nucleosome
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]
All Oct4 bound LIN28 nucleosomes
Sinha KK, Bilokapic S, Du Y, Malik D, Halic M
Nature (2023) 619 pp. 378-384 [ DOI: doi:10.1038/s41586-023-06112-6 Pubmed: 37225990 ]