9MPP
The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
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 (African clawed frog) | Histone H3 |
| 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 type 1 | polymer | 129 | 13978.2 | 2 | UniProt (P06897) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 4 | D, H (D, H) | Histone H2B 1.1 | polymer | 123 | 13655.9 | 2 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 5 | I (I) | DNA (167-MER) | polymer | 167 | 51327.7 | 1 | synthetic construct | ||
| 6 | J (J) | DNA (167-MER) | polymer | 167 | 51786.0 | 1 | synthetic construct | ||
| 7 | K, M (M, K) | DNA (cytosine-5)-methyltransferase 3A | polymer | 689 | 77914.7 | 2 | UniProt (Q9Y6K1) Pfam (PF00855) Pfam (PF17980) Pfam (PF21255) Pfam (PF00145) | Homo sapiens (human) | Dnmt3a,DNA methyltransferase HsaIIIA,M.HsaIIIA |
| 8 | L, N (N, L) | DNA (cytosine-5)-methyltransferase 3-like | polymer | 386 | 43534.6 | 2 | UniProt (Q9UJW3) Pfam (PF17980) Pfam (PF21255) | Homo sapiens (human) | |
| 9 | O, P, Q, S, T... (M, N) | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) | |||
| 10 | R, V (M, K) | S-ADENOSYL-L-HOMOCYSTEINE | non-polymer | 384.4 | 2 | Chemie (SAH) |
Sequence modifications
A, E: 1 - 135 (UniProt: P84233)
C, G: 1 - 129 (UniProt: P06897)
D, H: 1 - 122 (UniProt: P02281)
N, L: 1 - 386 (UniProt: Q9UJW3)
| PDB | External Database | Details |
|---|---|---|
| Ala 102 | Gly 103 | variant |
| PDB | External Database | Details |
|---|---|---|
| Arg 99 | Gly 100 | engineered mutation |
| Ser 123 | Ala 124 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Met 0 | - | initiating methionine |
| Thr 29 | Ser 33 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Thr 5 | Pro 5 | conflict |
| Gly 278 | Arg 278 | variant |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 14 |
| Total formula weight | 454677.4 | |
| Non-Polymers* | Number of molecules | 8 |
| Total formula weight | 1161.3 | |
| All* | Total formula weight | 455838.7 |
