6PWE: Nucleosome core particle
Cryo-EM structure of nucleosome core particle. Determined by electron microscopy at 3.95 Å resolution. Released 21 Aug 2019.
- Method
- Electron microscopy
- Resolution
- 3.95 Å
- Organisms
- Drosophila melanogaster, synthetic construct
- Chains
- 10
- Atoms
- 11,923
- Mol. weight
- 198.64 kDa
- Released
- 21 Aug 2019
Explore 6PWE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6PWE contains 38 α-helices and 14 β-strands across 8 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, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-49 | 3 | |
| α-helix | 65-74 | 10 | |
| α-helix | 89-104 | 16 | |
| α-helix | 109-112 | 4 | |
| β-strand | 118-119 | 2 | 1 |
| α-helix | 121-127 | 7 | |
Chain B: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-38 | 8 | |
| β-strand | 45-46 | 2 | 1 |
| α-helix | 50-62 | 13 | |
| α-helix | 67-75 | 9 | |
| α-helix | 83-92 | 10 | |
Chains C and G: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 29-32 | 4 | |
| β-strand | 41-42 | 2 | 2 |
| α-helix | 46-71 | 26 | |
| β-strand | 76-77 | 2 | 3 |
| α-helix | 79-87 | 9 | |
| α-helix | 90-93 | 4 | |
Chains D and H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-42 | 8 | |
| β-strand | 50-51 | 2 | 3 |
| α-helix | 55-79 | 25 | |
| β-strand | 85-86 | 2 | 2 |
| α-helix | 88-93 | 6 | |
| α-helix | 104-116 | 13 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 47-49 | 3 | |
| α-helix | 65-74 | 10 | |
| β-strand | 84 | 1 | 4 |
| α-helix | 89-104 | 16 | |
| α-helix | 109-112 | 4 | |
| β-strand | 118-119 | 2 | 5 |
| α-helix | 121-127 | 7 | |
Chain F: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-38 | 8 | |
| β-strand | 45-46 | 2 | 5 |
| α-helix | 50-62 | 13 | |
| α-helix | 67-75 | 9 | |
| β-strand | 81 | 1 | 4 |
| α-helix | 83-92 | 10 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3 | A, E | protein | 136 | Drosophila melanogaster | P02299 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Drosophila melanogaster | P84040 (AlphaFold model) |
| Histone H2A | C, G | protein | 124 | Drosophila melanogaster | P84051 (AlphaFold model) |
| Histone H2B | D, H | protein | 123 | Drosophila melanogaster | P02283 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | synthetic construct | |
| DNA (147-mer) | J | DNA | 147 | synthetic construct | |
Sequence of entity 1 (A, E), FASTA
>6PWE_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>6PWE_2 Histone H4 (chains B, F)
MTGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>6PWE_3 Histone H2A (chains C, G)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA
Sequence of entity 4 (D, H), FASTA
>6PWE_4 Histone H2B (chains D, H)
MPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK
Sequence of entity 5 (I), FASTA
>6PWE_5 DNA (147-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 6 (J), FASTA
>6PWE_6 DNA (147-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Primary citation
Structure of the primed state of the ATPase domain of chromatin remodeling factor ISWI bound to the nucleosome. Chittori, S., Hong, J., Bai, Y. et al. Nucleic Acids Res (2019) 47:9400-9409. DOI 10.1093/nar/gkz670 · PubMed
Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
- 6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
- 6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
- 7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
- 1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
- 9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
- 2NQB 2.3 Å, Drosophila Nucleosome Structure
- 9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
- 1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
- 2PYO 2.43 Å, Drosophila nucleosome core
- 8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
- 4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3
Browse structure collections
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