8OTS: OCT4 and MYC-MAX co-bound to a nucleosome
OCT4 and MYC-MAX co-bound to a nucleosome. Determined by electron microscopy at 3.3 Å resolution. Released 24 May 2023.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organisms
- Homo sapiens, synthetic construct, Aequorea victoria
- Chains
- 13
- Atoms
- 13,160
- Mol. weight
- 272.15 kDa
- Ligands
- PTD
- Released
- 24 May 2023
Explore 8OTS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8OTS contains 48 α-helices and 20 β-strands across 11 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 82 | 1 | |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 6 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 5 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 139 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 133 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 128 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (127-mer) | I | DNA | 127 | synthetic construct | |
| DNA (127-mer) | J | DNA | 127 | synthetic construct | |
| Green fluorescent protein,POU domain, class 5, transcription factor 1 | K | protein | 544 | Aequorea victoria, Homo sapiens | P42212, Q01860 |
| Myc proto-oncogene protein | M | protein | 94 | Homo sapiens | P01106 |
| Protein max | N | protein | 82 | Homo sapiens | P61244 |
Sequence of entity 1 (A, E), FASTA
>8OTS_1 Histone H3.1 (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8OTS_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8OTS_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>8OTS_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSA
Sequence of entity 5 (I), FASTA
>8OTS_5 DNA (127-MER) (chains I)
CTTTGTTATGCAAATCGGGGTGGGGCGTCGTAGACAGCTCTAGCACCGCTTAAACGCACG
TACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGT
GTCAGAT
Sequence of entity 6 (J), FASTA
>8OTS_6 DNA (127-MER) (chains J)
ATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACA
GCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACGCCCCACCCCGATTTGCAT
AACAAAG
Sequence of entity 7 (K), FASTA
>8OTS_7 Green fluorescent protein,POU domain, class 5, transcription factor 1 (chains K)
MDWSHPQFEKSAVDENLYFQGGMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDA
TYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERT
IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQ
KNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDH
MVLLEFVTAAGITLGMDELYKEAAAKEAAAKMAGHLASDFAFSPPPGGGGDGPGGPEPGW
VDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGG
LETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQF
AKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVE
EADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGL
EKDV
Sequence of entity 8 (M), FASTA
>8OTS_8 Myc proto-oncogene protein (chains M)
MHHHHHHEENVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYI
LSVQAEEQKLISEEDLLRKRREQLKHKLEQLRNS
Sequence of entity 9 (N), FASTA
>8OTS_9 Protein max (chains N)
MADKRAHHNALERKRRDHIKDSFHSLRDSVPSLQGEKASRAQILDKATEYIQYMRRKNHT
HQQDIDDLKRQNALLEQQVRAL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PTD | Pentanedial | C5 H8 O2 | 8 |
Primary citation
Cooperation between bHLH transcription factors and histones for DNA access. Michael, A.K., Stoos, L., Crosby, P. et al. Nature (2023) 619:385-393. DOI 10.1038/s41586-023-06282-3 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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