9V9R
Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E (A, E) | Histone H3 | polymer | 136 | 15435.1 | 2 | UniProt (A0A310TTQ1) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 2 | B, F (B, F) | Histone H4 | polymer | 103 | 11394.4 | 2 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 3 | C, G (C, G) | Histone H2A | polymer | 130 | 14109.4 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 4 | D, H (D, H) | Histone H2B | polymer | 126 | 13913.2 | 2 | UniProt (A0A8J0TWI5) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 5 | I (I) | DNA (144-MER) | polymer | 144 | 44217.2 | 1 | Homo sapiens | ||
| 6 | J (J) | DNA (145-MER) | polymer | 145 | 44992.6 | 1 | Homo sapiens | ||
| 7 | K (N) | E3 ubiquitin-protein ligase RING2 | polymer | 336 | 37706.4 | 1 | UniProt (Q99496) Pfam (PF13923) Pfam (PF16207) | Homo sapiens (human) | Huntingtin-interacting protein 2-interacting protein 3,HIP2-interacting protein 3,Protein DinG,RING finger protein 1B,RING1b,RING finger protein 2,RING finger protein BAP-1,RING-type E3 ubiquitin transferase RING2 |
| 8 | L (P) | Ubiquitin-conjugating enzyme E2 D3 | polymer | 147 | 16760.2 | 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 | M (O) | Ubiquitin | polymer | 76 | 8622.9 | 1 | UniProt (P0CG47) Pfam (PF00240) | Homo sapiens (human) | |
| 10 | N (R) | Ubiquitin | polymer | 76 | 8576.8 | 1 | UniProt (P62979) Pfam (PF00240) | Homo sapiens (human) | |
| 11 | O (M) | Polycomb group RING finger protein 1 | polymer | 259 | 30394.4 | 1 | UniProt (Q9BSM1) Pfam (PF13923) Pfam (PF16207) | Homo sapiens (human) | Nervous system Polycomb-1,NSPc1,RING finger protein 68 |
| 12 | P, Q, R, S (N, M) | ZINC ION | non-polymer | 65.4 | 4 | Chemie (ZN) PubChem (32051) |
Sequence modifications
D, H: -3 - 122 (UniProt: A0A8J0TWI5)
P: 1 - 147 (UniProt: P61077)
O: 1 - 76 (UniProt: P0CG47)
| PDB | External Database | Details |
|---|---|---|
| Cys 117 | Lys 121 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Arg 22 | Ser 22 | engineered mutation |
| Ser 85 | Cys 85 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Cys 76 | Gly 228 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 15 |
| Total formula weight | 300974.9 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 261.6 | |
| All* | Total formula weight | 301236.6 |
