4R8P
Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle
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 H3.2 | polymer | 135 | 15303.9 | 2 | UniProt (P84233) Pfam (PF00125) | Xenopus laevis (clawed frog common platanna platanna) | |
| 2 | B, F (B, F) | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (clawed frog common platanna platanna) | |
| 3 | C, G (C, G) | Histone H2A | polymer | 129 | 13978.2 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) UniProt (by SIFTS) (P06897) | Xenopus laevis (clawed frog common platanna platanna) | |
| 4 | D, H (D, H) | Histone H2B 1.1 | polymer | 122 | 13524.8 | 2 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (clawed frog common platanna platanna) | H2B1.1 |
| 5 | I (I) | DNA (147-mer) | polymer | 147 | 45138.8 | 1 | Synthetic DNA | ||
| 6 | J (J) | DNA (147-mer) | polymer | 147 | 45610.0 | 1 | Synthetic DNA | ||
| 7 | K, M (K, M) | Polycomb complex protein BMI-1 | polymer | 110 | 12595.7 | 2 | UniProt (P35226) Pfam (PF13923) | Homo sapiens (human) | Polycomb group RING finger protein 4, RING finger protein 51 |
| 8 | L, N (L, N) | E3 ubiquitin-protein ligase RING2, Ubiquitin-conjugating enzyme E2 D3 | polymer | 268 | 30118.6 | 2 | UniProt (Q99496) UniProt (P61077) Pfam (PF13923) Pfam (PF00179) | 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, Ubiquitin carrier protein D3, Ubiquitin-conjugating enzyme E2(17)KB 3, Ubiquitin-conjugating enzyme E2-17 kDa 3, Ubiquitin-protein ligase D3 |
| 9 | O, P, Q, R, S... (K, L, M, N) | ZINC ION | non-polymer | 65.4 | 8 | Chemie (ZN) |
Sequence modifications
A, E: 1 - 135 (UniProt: P84233)
D, H: 4 - 125 (UniProt: P02281)
K, M: 2 - 109 (UniProt: P35226)
L, N: 2 - 116 (UniProt: Q99496)
L, N: 202 - 347 (UniProt: P61077)
| PDB | External Database | Details |
|---|---|---|
| Ala 102 | Gly 103 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Thr 32 | Ser 33 | conflict |
| PDB | External Database | Details |
|---|---|---|
| Gly 0 | - | expression tag |
| Ser 1 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly 1 | - | expression tag |
| Gly 117 | - | linker |
| Ser 118 | - | linker |
| Gly 119 | - | linker |
| Ser 120 | - | linker |
| Arg 121 | - | linker |
| Ser 122 | - | linker |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 284317.9 | |
| Non-Polymers* | Number of molecules | 8 |
| Total formula weight | 523.3 | |
| All* | Total formula weight | 284841.2 |
