9IPU: RNF168(1-193)/UbcH5c-Ub ubiquitylation module
cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome. Determined by electron microscopy at 4.3 Å resolution. Released 2 Oct 2024.
- Method
- Electron microscopy
- Resolution
- 4.3 Å
- Organism
- Homo sapiens
- Chains
- 14
- Atoms
- 15,750
- Mol. weight
- 282.99 kDa
- Ligands
- ZN
- Released
- 2 Oct 2024
Explore 9IPU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9IPU contains 54 α-helices and 42 β-strands across 12 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 | 2 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 3 |
| 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 | 3 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 2 |
| α-helix | 83-91 | 9 | |
| β-strand | 97-98 | 2 | 4 |
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 | 5 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 6 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-102 | 3 | 7 |
Chain D: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 32-34 | 3 | |
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 6 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 5 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 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 | 8 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 9 |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-28 | 5 | |
| α-helix | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 9 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 8 |
| α-helix | 83-91 | 9 | |
| β-strand | 96-98 | 3 | 7 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42-43 | 2 | 10 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 11 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101-102 | 2 | 4 |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53-54 | 2 | 11 |
| α-helix | 56-83 | 28 | |
| β-strand | 88-89 | 2 | 10 |
| α-helix | 91-101 | 11 | |
| α-helix | 105-123 | 19 | |
4 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 H1.0 | I | protein | 194 | Homo sapiens | P07305 (AlphaFold model) |
| Histone H3.2 | A, E | protein | 135 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 102 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 129 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-K | D, H | protein | 125 | Homo sapiens | O60814 |
| Ubiquitin-conjugating enzyme E2 D3 | K | protein | 147 | Homo sapiens | P61077 |
| E3 ubiquitin-protein ligase RNF168 | L | protein | 193 | Homo sapiens | Q8IYW5 |
| Ubiquitin | M | protein | 75 | Homo sapiens | P62979 |
| DNA (171-mer) | J | DNA | 171 | Homo sapiens | |
| DNA (171-mer) | N | DNA | 171 | Homo sapiens | |
Sequence of entity 1 (I), FASTA
>9IPU_1 Histone H1.0 (chains I)
MTENSTSAPAAKPKRAKASKKSTDHPKYSDMIVAAIQAEKNRAGSSRQSIQKYIKSHYKV
GENADSQIKLSIKRLVTTGVLCQTKGVGASGSFRLAKSDEPKKSVAFKKTKKEIKKVATP
KKASKPKKAASKAPTKKPKATPVKKAKKKLAATPKKAKKPKTVKAKPVKASKPKKAKPVK
PKAKSSAKRAGKKK
Sequence of entity 2 (A, E), FASTA
>9IPU_2 Histone H3.2 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLSAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 3 (B, F), FASTA
>9IPU_3 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 4 (C, G), FASTA
>9IPU_4 Histone H2A type 1-B/E (chains C, G)
SGRGKQGGKARAKACTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 5 (D, H), FASTA
>9IPU_5 Histone H2B type 1-K (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSAK
Sequence of entity 6 (K), FASTA
>9IPU_6 Ubiquitin-conjugating enzyme E2 D3 (chains K)
MALKRINKELSDLARDPPAQSSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDY
PFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSISSLLSDPNPDDPLV
PEIARIYKTDRDKYNRISREWTQKYAM
Sequence of entity 7 (L), FASTA
>9IPU_7 E3 ubiquitin-protein ligase RNF168 (chains L)
MALPKDAIPSLSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVSS
WTRYHTRRNSLVNVELWTIIQKHYPRECKLRASGQESEEVADDYQPVRLLSKPGELRREY
EEEISKVAAERRASEEEENKASEEYIQRLLAEEEEEEKRQAEKRRRAMEEQLKSDEELAR
KLSIDINNFCEGS
Sequence of entity 8 (M), FASTA
>9IPU_8 Ubiquitin (chains M)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRG
Sequence of entity 9 (J), FASTA
>9IPU_9 DNA (171-MER) (chains J)
TTGGCCAGCTAGGATATCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCT
CTAGCACCGCTTAAACGCACGTACGGAATCCGTACGTGCGTTTAAGCGGTGCTAGAGCTG
TCTACGACCAATTGAGCGGCCTCGGCACCGGGATTGTGATATCCTAGCTGG
Sequence of entity 10 (N), FASTA
>9IPU_10 DNA (171-MER) (chains N)
CCAGCTAGGATATCACAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGGATTCCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTGTGATATCCTAGCTGGCCAA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 2 |
Primary citation
Promotion of RNF168-Mediated Nucleosomal H2A Ubiquitylation by Structurally Defined K63-Polyubiquitylated Linker Histone H1. Shi, Q., Deng, Z., Zhang, L. et al. Angew Chem Int Ed Engl (2025) 64:e202413651-e202413651. DOI 10.1002/anie.202413651 · PubMed
Other PDB entries of the same protein (UniProt P07305 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7COW 2.86 Å, 353 bp di-nucleosome harboring cohesive DNA termini with linker histone H1.0
- 7K5X 2.93 Å, Cryo-EM structure of a chromatosome containing human linker histone H1.0
- 6LAB 3.2 Å, 169 bp nucleosome, harboring cohesive DNA termini, assembled with linker histone H1.0
- 7XX6 3.39 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169a DNA fragment)
- 6LA8 3.4 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
- 7XVL 3.51 Å, Crystal Structure of Nucleosome-H1.0 Linker Histone Assembly (sticky-169an DNA fragment)
- 30FM 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
- 30HD 3.6 Å, Structure of histone H1 in an import-chaperone complex with importin beta and importin 7…
- 6LA9 3.7 Å, 349 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0…
- 6LA2 3.89 Å, 343 bp di-nucleosome harboring cohesive DNA termini assembled with linker histone H1.0
- 8TB9 4.0 Å, PRC2-J119-450 monomer bound to H1-nucleosome
- 7DBP 4.5 Å, Linker histone defines structure and self-association behaviour of the 177 bp human…
Browse structure collections
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