12OG
Cryo-EM structure of Arabidopsis VIM1 in complex with hemi-methylated CG-containing nucleosome 2
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, B (B, C) | Histone H2A | polymer | 130 | 14109.4 | 2 | UniProt (Q6AZJ8) | Xenopus laevis (African clawed frog) | |
| 2 | C, D (D, E) | Histone H2B 1.1 | polymer | 123 | 13655.9 | 2 | UniProt (P02281) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 3 | E, F (F, G) | Histone H3.2 | polymer | 136 | 15435.1 | 2 | UniProt (P84233) | Xenopus laevis (African clawed frog) | Histone H3 |
| 4 | G, H (H, I) | Histone H4 | polymer | 103 | 11394.4 | 2 | UniProt (P62798) | Xenopus laevis (African clawed frog) | |
| 5 | I (A) | E3 ubiquitin-protein ligase ORTHRUS 2 | polymer | 515 | 57670.4 | 1 | UniProt (Q8VYZ0) | Arabidopsis thaliana (thale cress) | Protein VARIANT IN METHYLATION 1,RING-type E3 ubiquitin transferase ORTHRUS 2 |
| 6 | J (L) | DNA | polymer | 211 | 65192.6 | 1 | Homo sapiens | ||
| 7 | K (M) | DNA | polymer | 211 | 65107.5 | 1 | Homo sapiens | ||
| 8 | L, M, N (A) | ZINC ION | non-polymer | 65.4 | 3 | Chemie (ZN) PubChem (32051) |
Sequence modifications
D, E: 1 - 122 (UniProt: P02281)
F, G: 0 - 135 (UniProt: P84233)
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
| Thr 29 | Ser 33 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Ala 102 | Gly 103 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 11 |
| Total formula weight | 297160.4 | |
| Non-Polymers* | Number of molecules | 3 |
| Total formula weight | 196.2 | |
| All* | Total formula weight | 297356.6 |
