8SPU: ESRRB nucleosome bound OCT4 at site c
Structure of ESRRB nucleosome bound OCT4 at site c. Determined by electron microscopy at 2.8 Å resolution. Released 28 Jun 2023.
- Method
- Electron microscopy
- Resolution
- 2.8 Å
- Organisms
- Homo sapiens, Escherichia coli
- Chains
- 13
- Atoms
- 16,181
- Mol. weight
- 332.67 kDa
- Released
- 28 Jun 2023
Explore 8SPU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8SPU contains 49 α-helices and 74 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 | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 6 |
Chain C: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| 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 | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| β-strand | 54-55 | 2 | 10 |
| α-helix | 57-84 | 28 | |
| β-strand | 89-90 | 2 | 9 |
| α-helix | 92-102 | 11 | |
| α-helix | 105-124 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-76 | 13 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
Chain F: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 3 |
Chain G: 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 | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 39-49 | 11 | |
| 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 | |
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 |
|---|
| DNA (168-mer) | J | DNA | 168 | Homo sapiens | |
| DNA (168-mer) | I | DNA | 168 | Homo sapiens | |
| Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 | L | protein | 550 | Homo sapiens | Q01860 (AlphaFold model) |
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-C | C, G | protein | 129 | Homo sapiens | Q16777 (AlphaFold model) |
| Histone H2B type 2-E | D, H | protein | 126 | Homo sapiens | Q16778 |
| ScFv | K, N | protein | 265 | Escherichia coli | |
Sequence of entity 1 (J), FASTA
>8SPU_1 DNA (168-MER) (chains J)
GCGTGCTGATTCCCTCCATTCGCTCTGCATAACTATCACTTTCTGGAACTCCATGGTCTC
CTAGGTCGCCAGGCCTTTGCTTTGCAGCTTAGAACAGACTCTCTATGCTCCCTCCACCCT
CTGTTTCTCCAGGTCCCACATGGGGAGGCGCTCCTTCTCCCTGCTGAT
Sequence of entity 2 (I), FASTA
>8SPU_2 DNA (168-MER) (chains I)
ATCAGCAGGGAGAAGGAGCGCCTCCCCATGTGGGACCTGGAGAAACAGAGGGTGGAGGGA
GCATAGAGAGTCTGTTCTAAGCTGCAAAGCAAAGGCCTGGCGACCTAGGAGACCATGGAG
TTCCAGAAAGTGATAGTTATGCAGAGCGAATGGAGGGAATCAGCACGC
Sequence of entity 3 (L), FASTA
>8SPU_3 Maltodextrin-binding protein,POU domain, class 5, transcription factor 1 (chains L)
MKEAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDG
PDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLI
YNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKY
DIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNID
TSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKD
KPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQT
VDAALAAAQTNAGSENLYFQGSVDSAAASDIKALQKELEQFAKLLKQKRITLGYTQADVG
LTLGVLFGKVFSQTTICRFEALQLSFKNMCKLRPLLQKWVEEADNNENLQEICKAETLVQ
ARKRKRTSIENRVRGNLENLFLQCPKPTLQQISHIAQQLGLEKDVVRVWFCNRRQKGKRS
SSEFHHHHHH
Sequence of entity 4 (A, E), FASTA
>8SPU_4 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 5 (B, F), FASTA
>8SPU_5 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 6 (C, G), FASTA
>8SPU_6 Histone H2A type 2-C (chains C, G)
MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKK
TESHKAKSK
Sequence of entity 7 (D, H), FASTA
>8SPU_7 Histone H2B type 2-E (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 8 (K, N), FASTA
>8SPU_8 ScFv (chains K, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA
Primary citation
Structural mechanism of LIN28B nucleosome targeting by OCT4. Guan, R., Lian, T., Zhou, B.R. et al. Mol Cell (2023) 83:1970-1982.e6. DOI 10.1016/j.molcel.2023.05.030 · PubMed
Other PDB entries of the same protein (UniProt Q01860 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8G88 2.3 Å, Human Oct4 bound to nucleosome with human nMatn1 sequence
- 7U0G 2.6 Å, structure of LIN28b nucleosome bound 3 OCT4
- 7U0I 2.6 Å, Structure of LIN28b nucleosome bound 2 OCT4
- 8SPS 3.0 Å, High resolution structure of ESRRB nucleosome bound OCT4 at site a and site b
- 6T90 3.05 Å, OCT4-SOX2-bound nucleosome - SHL-6
- 8G8G 3.2 Å, Interaction of H3 tail in LIN28B nucleosome with Oct4
- 8OTS 3.3 Å, OCT4 and MYC-MAX co-bound to a nucleosome
- 6YOV 3.42 Å, OCT4-SOX2-bound nucleosome - SHL+6
- 9RL4 3.5 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL-6
- 8G8E 3.9 Å, Human Oct4 bound to nucleosome with human LIN28B sequence
- 9RN2 4.1 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 2
- 9RMC 4.2 Å, Structure of BAF in complex with OCT4-SOX2-bound nucleosome - SHL+6 class 1
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