8UPF: Human nucleosome core particle
Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c. 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
- 14,012
- Mol. weight
- 228.3 kDa
- Ligands
- ZN
- Released
- 17 Jan 2024
Explore 8UPF in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8UPF contains 48 α-helices and 34 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.
Chains A and E: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 46-55 | 10 | |
| 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 | 25-28 | 4 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 3 |
Chain C: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| β-strand | 42-43 | 2 | 5 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 4 |
| α-helix | 80-89 | 10 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 8 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 31-33 | 3 | |
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 4 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
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 | 83-93 | 11 | |
| β-strand | 97-98 | 2 | 8 |
Chain G: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 9 |
| α-helix | 80-89 | 10 | |
| α-helix | 93-96 | 4 | |
| β-strand | 101-102 | 2 | 3 |
| α-helix | 113-115 | 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 | 10 |
| α-helix | 91-101 | 11 | |
| α-helix | 104-122 | 19 | |
Chain K: 4 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15 | 1 | 11 |
| β-strand | 22 | 1 | 11 |
| β-strand | 26-28 | 3 | 12 |
| β-strand | 34-36 | 3 | 12 |
| α-helix | 37-45 | 9 | |
| β-strand | 50 | 1 | 13 |
| β-strand | 57 | 1 | 13 |
| α-helix | 59-66 | 8 | |
| β-strand | 72 | 1 | 12 |
| α-helix | 74-83 | 10 | |
| α-helix | 85-92 | 8 | |
1 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 H2B type 1-J | D, H | protein | 119 | 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 | 101 | Homo sapiens | Q8IYW5 (AlphaFold model) |
| Ubiquitin-conjugating enzyme E2 D3 | L | protein | 174 | Homo sapiens | P61077 |
| Histone H2A type 1-B/E | C, G | protein | 119 | Homo sapiens | P04908 |
Sequence of entity 1 (A, E), FASTA
>8UPF_1 Histone H3.1 (chains A, E)
GPGHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQ
KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAK
RVTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>8UPF_2 Histone H4 (chains B, F)
GPGHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETR
GVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (D, H), FASTA
>8UPF_3 Histone H2B type 1-J (chains D, H)
KSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNS
FVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
Sequence of entity 4 (I), FASTA
>8UPF_4 DNA (147-MER) (chains I)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT
Sequence of entity 5 (J), FASTA
>8UPF_5 DNA (147-MER) (chains J)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT
Sequence of entity 6 (K), FASTA
>8UPF_6 E3 ubiquitin-protein ligase RNF168 (chains K)
GHMALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRV
SSWTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGSGSGS
Sequence of entity 7 (L), FASTA
>8UPF_7 Ubiquitin-conjugating enzyme E2 D3 (chains L)
GSALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTD
YPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPL
VPEIARIYKTDRDKYNRISREWTQKYAMGSGSGSGGSGGGSGGSGGSGGSGSGS
Sequence of entity 8 (C, G), FASTA
>8UPF_8 Histone H2A type 1-B/E (chains C, G)
SAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAA
RDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK
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
About this viewer
MolViewer shows 8UPF directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.