9IPU
cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (I) | Histone H1.0 | polymer | 194 | 20901.1 | 1 | UniProt (P07305) Pfam (PF00538) | Homo sapiens (human) | Histone H1',Histone H1(0) |
| 2 | B, F (A, E) | Histone H3.2 | polymer | 135 | 15273.8 | 2 | UniProt (Q71DI3) Pfam (PF00125) | Homo sapiens (human) | H3-clustered histone 13,H3-clustered histone 14,H3-clustered histone 15,Histone H3/m,Histone H3/o |
| 3 | C, G (B, F) | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (P62805) Pfam (PF15511) | Homo sapiens (human) | |
| 4 | D, H (C, G) | Histone H2A type 1-B/E | polymer | 129 | 14008.3 | 2 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 5 | E, I (D, H) | Histone H2B type 1-K | polymer | 125 | 13790.0 | 2 | UniProt (O60814) Pfam (PF00125) | Homo sapiens (human) | H2B K,HIRA-interacting protein 1 |
| 6 | J (K) | Ubiquitin-conjugating enzyme E2 D3 | polymer | 147 | 16657.9 | 1 | UniProt (P61077) Pfam (PF00179) | Homo sapiens (human) | (E3-independent) E2 ubiquitin-conjugating enzyme D3,E2 ubiquitin-conjugating enzyme D3,Ubiquitin carrier protein D3,Ubiquitin-conjugating enzyme E2(17)KB 3,Ubiquitin-conjugating enzyme E2-17 kDa 3,Ubiquitin-protein ligase D3 |
| 7 | K (L) | E3 ubiquitin-protein ligase RNF168 | polymer | 193 | 22533.5 | 1 | UniProt (Q8IYW5) Pfam (PF14447) | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
| 8 | L (M) | Ubiquitin | polymer | 75 | 8519.8 | 1 | UniProt (P62979) Pfam (PF00240) | Homo sapiens (human) | |
| 9 | M (J) | DNA (171-MER) | polymer | 171 | 52825.7 | 1 | Homo sapiens (human) | ||
| 10 | N (N) | DNA (171-MER) | polymer | 171 | 52754.6 | 1 | Homo sapiens (human) | ||
| 11 | O, P (L) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
I: 1 - 194 (UniProt: P07305)
A, E: 1 - 135 (UniProt: Q71DI3)
C, G: 1 - 129 (UniProt: P04908)
K: 1 - 147 (UniProt: P61077)
| PDB | External Database | Details |
|---|---|---|
| Cys 82 | Lys 82 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 110 | Cys 111 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Cys 15 | Lys 16 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Ser 21 | Cys 21 | conflict |
| Ser 107 | Cys 107 | conflict |
| Ser 111 | Cys 111 | conflict |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 282863.5 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 130.8 | |
| All* | Total formula weight | 282994.3 |
