8X7K: RNF168/UbcH5c-Ub
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination). Determined by electron microscopy at 3.27 Å resolution. Released 7 Aug 2024.
- Method
- Electron microscopy
- Resolution
- 3.27 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 13,387
- Mol. weight
- 203.81 kDa
- Ligands
- ZN
- Released
- 7 Aug 2024
Explore 8X7K in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8X7K contains 44 α-helices and 30 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 | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| 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 | 50-76 | 27 | |
| β-strand | 80-81 | 2 | 1 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 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 | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 6 |
Chain D: 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 | 104-122 | 19 | |
Chain E: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 83-84 | 2 | 7 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 8 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 23-28 | 6 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 8 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 7 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 6 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 10 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 3 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 10 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 9 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
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 H3.2 | A, E | protein | 97 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 82 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C | protein | 105 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 94 | Homo sapiens | O60814 (AlphaFold model) |
| Histone H2A type 1-B/E | G | protein | 108 | Homo sapiens | P04908 (AlphaFold model) |
| DNA (143-mer) | I | DNA | 143 | Homo sapiens | |
| DNA (143-mer) | J | DNA | 143 | Homo sapiens | |
| Ubiquitin-conjugating enzyme E2 D3 | K | protein | 147 | Homo sapiens | P61077 |
| E3 ubiquitin-protein ligase RNF168 | L | protein | 113 | Homo sapiens | Q8IYW5 |
Sequence of entity 1 (A, E), FASTA
>8X7K_1 Histone H3.2 (chains A, E)
PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASE
AYLVGLFEDTNLSAIHAKRVTIMPKDIQLARRIRGER
Sequence of entity 2 (B, F), FASTA
>8X7K_2 Histone H4 (chains B, F)
KVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRK
TVTAMDVVYALKRQGRTLYGFG
Sequence of entity 3 (C), FASTA
>8X7K_3 Histone H2A type 1-B/E (chains C)
ACTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPK
Sequence of entity 4 (D, H), FASTA
>8X7K_4 Histone H2B type 1-K (chains D, H)
RSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA
Sequence of entity 5 (G), FASTA
>8X7K_5 Histone H2A type 1-B/E (chains G)
ARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNA
ARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP
Sequence of entity 6 (I), FASTA
>8X7K_6 DNA (143-MER) (chains I)
CAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAA
ACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGA
GCGGCCTCGGCACCGGGATTCTC
Sequence of entity 7 (J), FASTA
>8X7K_7 DNA (143-MER) (chains J)
GAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACG
CACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGC
ACGTGTCAGATATATACATCCTG
Sequence of entity 8 (K), FASTA
>8X7K_8 Ubiquitin-conjugating enzyme E2 D3 (chains K)
MALKRINKELSDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLV
PEIARIYKTDRDKYNRISREWTQKYAM
Sequence of entity 9 (L), FASTA
>8X7K_9 E3 ubiquitin-protein ligase RNF168 (chains L)
MALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS
WTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADDYQPVRLLSKP
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168. Ai, H., Tong, Z., Deng, Z. et al. bioRxiv (2024). DOI 10.1101/2024.01.02.573964
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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