8PKI: NR5A2-nucleosome complex SHL+5.5
Cryo-EM structure of NR5A2-nucleosome complex SHL+5.5. Determined by electron microscopy at 2.58 Å resolution. Released 28 Feb 2024.
- Method
- Electron microscopy
- Resolution
- 2.58 Å
- Organisms
- Mus musculus, synthetic construct, Homo sapiens
- Chains
- 11
- Atoms
- 11,957
- Mol. weight
- 215.23 kDa
- Ligands
- ZN
- Released
- 28 Feb 2024
Explore 8PKI in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PKI contains 39 α-helices and 22 β-strands across 9 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: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| 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 | 2 |
| α-helix | 50-74 | 25 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 96-98 | 3 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| 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 | 100-102 | 3 | 6 |
Chains D and H: 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 | 104-123 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-76 | 13 | |
| 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 | 24-27 | 4 | |
| α-helix | 30-39 | 10 | |
| β-strand | 44-45 | 2 | 8 |
| α-helix | 49-74 | 26 | |
| β-strand | 79-80 | 2 | 7 |
| α-helix | 82-91 | 10 | |
| β-strand | 95-97 | 3 | 6 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| 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 | 100-102 | 3 | 3 |
Chain K: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 95-97 | 3 | 11 |
| β-strand | 100-102 | 3 | 11 |
| α-helix | 104-116 | 13 | |
| α-helix | 133-136 | 4 | |
| α-helix | 139-148 | 10 | |
| α-helix | 169-177 | 9 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.3 | A, E | protein | 136 | Mus musculus | P84244 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Mus musculus | P62806 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Mus musculus | C0HKE3 (AlphaFold model) |
| Histone H2B type 1-C/E/G | D, H | protein | 126 | Mus musculus | Q6ZWY9 (AlphaFold model) |
| DNA | I | DNA | 153 | synthetic construct | |
| DNA | J | DNA | 153 | synthetic construct | |
| Nuclear receptor subfamily 5 group A member 2 | K | protein | 94 | Homo sapiens | O00482 |
Sequence of entity 1 (A, E), FASTA
>8PKI_1 Histone H3.3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8PKI_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8PKI_3 Histone H2A (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>8PKI_4 Histone H2B type 1-C/E/G (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK
Sequence of entity 5 (I), FASTA
>8PKI_5 DNA (chains I)
ATCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCT
TAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCT
CCAGGCACGTTCAAGGCCAATACATCCTGTGAT
Sequence of entity 6 (J), FASTA
>8PKI_6 DNA (chains J)
ATCACAGGATGTATTGGCCTTGAACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGT
TAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAA
TTGAGCGGCCTCGGCACCGGGATTCTCCAGGAT
Sequence of entity 7 (K), FASTA
>8PKI_7 Nuclear receptor subfamily 5 group A member 2 (chains K)
LCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQ
KCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRAL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 1 |
Primary citation
Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition. Kobayashi, W., Sappler, A.H., Bollschweiler, D. et al. Nat Struct Mol Biol (2024) 31:757-766. DOI 10.1038/s41594-024-01239-0 · PubMed
Other PDB entries of the same protein (UniProt P84244 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8PKJ 2.5 Å, Cryo-EM structure of the nucleosome containing Nr5a2 motif at SHL+5.5
- 5XM0 2.87 Å, The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4
- 5XM1 3.45 Å, The mouse nucleosome structure containing H2A, H2B type3-A, H3mm7, and H4
- 2RVN Solution structure of the chromodomain of HP1a with the phosphorylated N-terminal tail…
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