8SMY: Human nucleosome core particle
Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (class 3). Determined by electron microscopy at 3.2 Å resolution. Released 17 Jan 2024.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 13,998
- Mol. weight
- 229.09 kDa
- Ligands
- ZN
- Released
- 17 Jan 2024
Explore 8SMY in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8SMY contains 49 α-helices and 31 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 | 41-42 | 2 | |
| α-helix | 47-54 | 8 | |
| α-helix | 64-74 | 11 | |
| 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 | 31-41 | 11 | |
| 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, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 4 |
| α-helix | 47-72 | 26 | |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 5 |
Chain D: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-33 | 3 | |
| α-helix | 38-48 | 11 | |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 4 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 47-54 | 8 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 6 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 7 |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 7 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 6 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 5 |
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 | 8 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 100-102 | 3 | 3 |
| α-helix | 117-118 | 2 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 9 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 8 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-121 | 18 | |
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, E | protein | 140 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 107 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 119 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 128 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (147-mer) | I | DNA | 147 | Homo sapiens | |
| DNA (147-mer) | J | DNA | 147 | Homo sapiens | |
| E3 ubiquitin-protein ligase RNF168 | K | protein | 103 | Homo sapiens | Q8IYW5 |
| Ubiquitin-conjugating enzyme E2 D3 | L | protein | 151 | Homo sapiens | P61077 |
Sequence of entity 1 (A, E), FASTA
>8SMY_1 Histone H3.1 (chains A, E)
GPGHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQ
KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAK
RVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8SMY_2 Histone H4 (chains B, F)
GPGHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETR
GVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>8SMY_3 Histone H2A type 1-B/E (chains C, G)
SAKACTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>8SMY_4 Histone H2B type 1-J (chains D, H)
GPGHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGIS
SKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGT
KAVTKYTS
Sequence of entity 5 (I), FASTA
>8SMY_5 DNA (147-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 6 (J), FASTA
>8SMY_6 DNA (147-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 7 (K), FASTA
>8SMY_7 E3 ubiquitin-protein ligase RNF168 (chains K)
MGHHHHHHGSMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLC
CPFCRRRVSSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRAS
Sequence of entity 8 (L), FASTA
>8SMY_8 Ubiquitin-conjugating enzyme E2 D3 (chains L)
GPGHMALKRINKELSDLARDPPAQISAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHF
PTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSIASLLDDPNPD
DPKVPEIARIYKTDRDKYNRISREWTQKYAM
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Mechanisms of RNF168 nucleosome recognition and ubiquitylation. Hu, Q., Zhao, D., Cui, G. et al. Mol Cell (2024) 84:839-853.e12. DOI 10.1016/j.molcel.2023.12.036 · 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
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