8X7I
Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, D (A, E) | Histone H3.2 | polymer | 98 | 11530.4 | 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 |
| 2 | B, E (B, F) | Histone H4 | polymer | 83 | 9509.2 | 2 | UniProt (P62805) Pfam (PF15511) | Homo sapiens (human) | |
| 3 | C (C) | Histone H2A type 1-B/E | polymer | 111 | 12141.2 | 1 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 4 | F (G) | Histone H2A type 1-B/E | polymer | 109 | 11936.9 | 1 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 5 | G (I) | DNA (147-MER) | polymer | 147 | 45604.0 | 1 | Homo sapiens (human) | ||
| 6 | H (J) | DNA (147-MER) | polymer | 147 | 45145.8 | 1 | Homo sapiens (human) | ||
| 7 | I, J (D, H) | Histone H2B type 1-K | polymer | 94 | 10478.0 | 2 | UniProt (O60814) Pfam (PF00125) | Homo sapiens (human) | |
| 8 | K (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 |
| 9 | L (L) | E3 ubiquitin-protein ligase RNF168 | polymer | 113 | 12987.1 | 1 | UniProt (Q8IYW5) Pfam (PF14447) | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
| 10 | M (M) | Ubiquitin | polymer | 76 | 8622.9 | 1 | UniProt (P62979) Pfam (PF00240) | Homo sapiens (human) | |
| 11 | N, O (L) | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, E: 37 - 134 (UniProt: Q71DI3)
C: 10 - 120 (UniProt: P04908)
K: 1 - 147 (UniProt: P61077)
M: 1 - 75 (UniProt: P62979)
| 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 |
| PDB | External Database | Details |
|---|---|---|
| Cys 76 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 13 |
| Total formula weight | 216131.2 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 130.8 | |
| All* | Total formula weight | 216262.0 |
