8X7K
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E | Histone H3.2 | polymer | 97 | 11401.3 | 2 | UniProt (Q71DI3) Pfam (PF00125) In PDB | Homo sapiens (human) | H3-clustered histone 13,H3-clustered histone 14,H3-clustered histone 15,Histone H3/m,Histone H3/o |
| 2 | B, F | Histone H4 | polymer | 82 | 9352.0 | 2 | UniProt (P62805) Pfam (PF15511) In PDB | Homo sapiens (human) | |
| 3 | C | Histone H2A type 1-B/E | polymer | 105 | 11482.4 | 1 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 4 | D, H | Histone H2B type 1-K | polymer | 94 | 10478.0 | 2 | UniProt (O60814) Pfam (PF00125) In PDB | Homo sapiens (human) | H2B K,HIRA-interacting protein 1 |
| 5 | G | Histone H2A type 1-B/E | polymer | 108 | 11807.8 | 1 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 6 | I | DNA (143-MER) | polymer | 143 | 44359.2 | 1 | Homo sapiens (human) | ||
| 7 | J | DNA (143-MER) | polymer | 143 | 43919.0 | 1 | Homo sapiens (human) | ||
| 8 | K | Ubiquitin-conjugating enzyme E2 D3 | polymer | 147 | 16657.9 | 1 | UniProt (P61077) Pfam (PF00179) In PDB | 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 |
| 9 | L | E3 ubiquitin-protein ligase RNF168 | polymer | 113 | 12987.1 | 1 | UniProt (Q8IYW5) Pfam (PF14447) In PDB | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
| 10 | L | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, E: 38 - 134 (UniProt: Q71DI3)
C: 14 - 118 (UniProt: P04908)
K: 1 - 147 (UniProt: P61077)
| 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 | 12 |
| Total formula weight | 203676.0 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 130.8 | |
| All* | Total formula weight | 203806.8 |
