9BE6: Human Nucleosome collected by Leginon on Krios
Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution. Determined by electron microscopy at 3.0 Å resolution. Released 30 Apr 2025.
- Method
- Electron microscopy
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 10
- Atoms
- 11,163
- Mol. weight
- 174.3 kDa
- Released
- 30 Apr 2025
Explore 9BE6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9BE6 contains 37 α-helices and 20 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, 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 | |
Chains B and F: 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 | 50-75 | 26 | |
| 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 | 80-89 | 10 | |
| 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 | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-120 | 20 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 40-42 | 3 | |
| 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 G: 6 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 | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 113-115 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.2 | A | protein | 97 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B | protein | 83 | Homo sapiens | A0A9J8D176 (AlphaFold model) |
| Histone H2A type 1 | C | protein | 103 | Homo sapiens | P0C0S8 (AlphaFold model) |
| Histone H2B type 1-J | D | protein | 95 | Homo sapiens | P06899 (AlphaFold model) |
| Histone H3.2 | E | protein | 97 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | F | protein | 78 | Homo sapiens | P62805 |
| Histone H2A type 1-B/E | G | protein | 105 | Homo sapiens | P04908 |
| Histone H2B type 1-J | H | protein | 93 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (145-mer) | I | DNA | 145 | Homo sapiens | |
| DNA (145-mer) | J | DNA | 145 | Homo sapiens | |
Sequence of entity 1 (A), FASTA
>9BE6_1 Histone H3.2 (chains A)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B), FASTA
>9BE6_2 Histone H4 (chains B)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C), FASTA
>9BE6_3 Histone H2A type 1 (chains C)
TRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKK
TRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK
Sequence of entity 4 (D), FASTA
>9BE6_4 Histone H2B type 1-J (chains D)
KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
Sequence of entity 5 (E), FASTA
>9BE6_5 Histone H3.2 (chains E)
HRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEA
YLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Sequence of entity 6 (F), FASTA
>9BE6_6 Histone H4 (chains F)
NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAM
DVVYALKRQGRTLYGFGG
Sequence of entity 7 (G), FASTA
>9BE6_7 Histone H2A type 1-B/E (chains G)
AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDN
KKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK
Sequence of entity 8 (H), FASTA
>9BE6_8 Histone H2B type 1-J (chains H)
TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITS
REIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 9 (I), FASTA
>9BE6_9 DNA (145-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGAT
Sequence of entity 10 (J), FASTA
>9BE6_10 DNA (145-MER) (chains J)
ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTGAT
Primary citation
Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution. Jia, L., Ruben, E.A., Olsen, S.K. et al. To be published.
Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
- 2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
- 5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
- 6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- 7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
- 4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
- 4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Browse structure collections
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