8UPF
Cryo-EM structure of the human nucleosome core particle in complex with RNF168-UbcH5c
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 H3.1 | polymer | 140 | 15786.5 | 2 | UniProt (P68431) Pfam (PF00125) In PDB | Homo sapiens (human) | Histone H3/a,Histone H3/b,Histone H3/c,Histone H3/d,Histone H3/f,Histone H3/h,Histone H3/i,Histone H3/j,Histone H3/k,Histone H3/l |
| 2 | B, F | Histone H4 | polymer | 107 | 11743.8 | 2 | UniProt (P62805) Pfam (PF15511) In PDB | Homo sapiens (human) | |
| 3 | D, H | Histone H2B type 1-J | polymer | 119 | 13209.4 | 2 | UniProt (P06899) Pfam (PF00125) In PDB | Homo sapiens (human) | Histone H2B.1,Histone H2B.r,H2B/r |
| 4 | I | DNA (147-MER) | polymer | 147 | 45138.8 | 1 | Homo sapiens | ||
| 5 | J | DNA (147-MER) | polymer | 147 | 45610.0 | 1 | Homo sapiens | ||
| 6 | K | E3 ubiquitin-protein ligase RNF168 | polymer | 101 | 11370.3 | 1 | UniProt (Q8IYW5) Pfam (PF14447) In PDB | Homo sapiens (human) | hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168 |
| 7 | L | Ubiquitin-conjugating enzyme E2 D3 | polymer | 174 | 18502.7 | 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 |
| 8 | C, G | Histone H2A type 1-B/E | polymer | 119 | 13034.2 | 2 | UniProt (P04908) Pfam (PF00125) Pfam (PF16211) In PDB | Homo sapiens (human) | Histone H2A.2,Histone H2A/a,Histone H2A/m |
| 9 | K | ZINC ION | non-polymer | 65.4 | 2 | Chemie (ZN) |
Sequence modifications
A, E: 0 - 135 (UniProt: P68431)
B, F: 0 - 102 (UniProt: P62805)
K: 1 - 94 (UniProt: Q8IYW5)
L: 2 - 147 (UniProt: P61077)
C, G: 12 - 129 (UniProt: P04908)
| PDB | External Database | Details |
|---|---|---|
| Gly -4 | - | expression tag |
| Pro -3 | - | expression tag |
| Gly -2 | - | expression tag |
| His -1 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -4 | - | expression tag |
| Pro -3 | - | expression tag |
| Gly -2 | - | expression tag |
| His -1 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| His 0 | - | expression tag |
| Ser 95 | - | expression tag |
| Gly 96 | - | expression tag |
| Ser 97 | - | expression tag |
| Gly 98 | - | expression tag |
| Ser 99 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -2 | - | expression tag |
| Ser -1 | - | expression tag |
| Gly 148 | - | expression tag |
| Ser 149 | - | expression tag |
| Gly 150 | - | expression tag |
| Ser 151 | - | expression tag |
| Gly 152 | - | expression tag |
| Ser 153 | - | expression tag |
| Gly 154 | - | expression tag |
| Gly 155 | - | expression tag |
| Ser 156 | - | expression tag |
| Gly 157 | - | expression tag |
| Gly 158 | - | expression tag |
| Gly 159 | - | expression tag |
| Ser 160 | - | expression tag |
| Gly 161 | - | expression tag |
| Gly 162 | - | expression tag |
| Ser 163 | - | expression tag |
| Gly 164 | - | expression tag |
| Gly 165 | - | expression tag |
| Ser 166 | - | expression tag |
| Gly 167 | - | expression tag |
| Gly 168 | - | expression tag |
| Ser 169 | - | expression tag |
| Gly 170 | - | expression tag |
| Ser 171 | - | expression tag |
| Gly 172 | - | expression tag |
| Ser 173 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Ser 11 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 228169.6 | |
| Non-Polymers* | Number of molecules | 2 |
| Total formula weight | 130.8 | |
| All* | Total formula weight | 228300.4 |
