6YOV: OCT4-SOX2-bound nucleosome - SHL+6
OCT4-SOX2-bound nucleosome - SHL+6. Determined by electron microscopy at 3.42 Å resolution. Released 6 May 2020.
- Method
- Electron microscopy
- Resolution
- 3.42 Å
- Organisms
- Homo sapiens, synthetic construct, Aequorea victoria
- Chains
- 12
- Atoms
- 12,298
- Mol. weight
- 379.46 kDa
- Ligands
- PTD
- Released
- 6 May 2020
Explore 6YOV in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YOV contains 47 α-helices and 20 β-strands across 10 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 | 41-43 | 3 | |
| α-helix | 46-57 | 12 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 1 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 2 |
| α-helix | 122-131 | 10 | |
Chain B: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-29 | 4 | |
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 2 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 1 |
| α-helix | 83 | 1 | |
| α-helix | 84-92 | 9 | |
| β-strand | 97-99 | 3 | 3 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-21 | 4 | |
| α-helix | 28-36 | 9 | |
| β-strand | 43-44 | 2 | 4 |
| α-helix | 48-73 | 26 | |
| β-strand | 78-79 | 2 | 5 |
| α-helix | 81-90 | 10 | |
| α-helix | 92-97 | 6 | |
| β-strand | 101-103 | 3 | 6 |
| α-helix | 114-116 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-47 | 9 | |
| β-strand | 54-55 | 2 | 5 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 4 |
| α-helix | 92-102 | 11 | |
| α-helix | 105-122 | 18 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-43 | 3 | |
| α-helix | 46-55 | 10 | |
| α-helix | 65-76 | 12 | |
| β-strand | 84-85 | 2 | 7 |
| α-helix | 87-114 | 28 | |
| β-strand | 119-120 | 2 | 8 |
| α-helix | 122-132 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-41 | 10 | |
| β-strand | 46-47 | 2 | 8 |
| α-helix | 51-76 | 26 | |
| β-strand | 81-82 | 2 | 7 |
| α-helix | 83 | 1 | |
| α-helix | 84-92 | 9 | |
| β-strand | 97-99 | 3 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-22 | 5 | |
| α-helix | 28-34 | 7 | |
| β-strand | 43-44 | 2 | 9 |
| α-helix | 47-73 | 27 | |
| β-strand | 78-79 | 2 | 10 |
| α-helix | 81-90 | 10 | |
| α-helix | 94-97 | 4 | |
| β-strand | 101-103 | 3 | 3 |
| α-helix | 114-116 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-47 | 9 | |
| β-strand | 54-55 | 2 | 10 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 9 |
| α-helix | 92-102 | 11 | |
| α-helix | 105-123 | 19 | |
2 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 | protein | 139 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B | protein | 105 | 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) |
| Histone H3.1 | E | protein | 137 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | F | protein | 106 | Homo sapiens | P62805 (AlphaFold model) |
| DNA (142-mer) | I, J | DNA | 300 | synthetic construct | |
| Green fluorescent protein,POU domain, class 5, transcription factor 1 | K | protein | 631 | Aequorea victoria, Homo sapiens | P42212, Q01860 |
| Transcription factor SOX-2 | L | protein | 105 | Homo sapiens | P48431 |
Sequence of entity 1 (A), FASTA
>6YOV_1 Histone H3.1 (chains A)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B), FASTA
>6YOV_2 Histone H4 (chains B)
GSHMSGRGKGGKGLGKGGAKRHRVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGV
LKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6YOV_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>6YOV_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSA
Sequence of entity 5 (E), FASTA
>6YOV_5 Histone H3.1 (chains E)
GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGE
Sequence of entity 6 (F), FASTA
>6YOV_6 Histone H4 (chains F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 7 (I, J), FASTA
>6YOV_7 DNA (142-MER) (chains I, J)
ATCCTGGAGAATCCCGGTCTGCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCCTTTGTTATGCAAATACATCCTGTACAGGATGTATTTGCATAACAAAGGCCTGG
AGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTA
AGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTGCAGACCGGGATTCTCCAGGAT
Sequence of entity 8 (K), FASTA
>6YOV_8 Green fluorescent protein,POU domain, class 5, transcription factor 1 (chains K)
MDWSHPQFEKSAVDENLYFQGGMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDA
TYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERT
IFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQ
KNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDH
MVLLEFVTAAGITLGMDELYKEAAAKEAAAKMAGHLASDFAFSPPPGGGGDGPGGPEPGW
VDPRTWLSFQGPPGGPGIGPGVGPGSEVWGIPPCPPPYEFCGGMAYCGPQVGVGLVPQGG
LETSQPEGEAGVGVESNSDGASPEPCTVTPGAVKLEKEKLEQNPEESQDIKALQKELEQF
AKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVE
EADNNENLQEICKAETLVQARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGL
EKDVVRVWFCNRRQKGKRSSSDYAQREDFEAAGSPFSGGPVSFPLAPGPHFGTPGYGSPH
FTALYSSVPFPEGEAFPPVSVTTLGSPMHSN
Sequence of entity 9 (L), FASTA
>6YOV_9 Transcription factor SOX-2 (chains L)
MDWSHPQFEKSAVDENLYFQGGMSPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISK
RLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PTD | Pentanedial | C5 H8 O2 | 8 |
Primary citation
Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Michael, A.K., Grand, R.S., Isbel, L. et al. Science (2020) 368:1460-1465. DOI 10.1126/science.abb0074 · 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
About this viewer
MolViewer shows 6YOV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.