9Y4P
Cryo-EM structure of DNMT3A2/3B3 in complex with H3K36me2 di-nucleosome with eight base pair linker
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Histone H3 | polymer | 135 | 15331.0 | 1 | UniProt (A0A310TTQ1) Pfam (PF00125) | Xenopus laevis (African clawed frog) | |
| 2 | B, F, K, O (B, F, X, R) | Histone H4 | polymer | 103 | 11394.4 | 4 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 3 | C, G, L, P (C, G, Y, S) | Histone H2A type 1 | polymer | 129 | 13978.2 | 4 | UniProt (P06897) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 4 | D, H, M, Q (D, H, P, T) | Histone H2B 1.1 | polymer | 123 | 13655.9 | 4 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 5 | E, J, N (E, W, Q) | Histone H3.2 | polymer | 135 | 15303.9 | 3 | UniProt (P84233) Pfam (PF00125) | Xenopus laevis (African clawed frog) | Histone H3 |
| 6 | I (I) | DNA (321-MER) | polymer | 321 | 99578.2 | 1 | Homo sapiens | ||
| 7 | R (J) | DNA (321-MER) | polymer | 321 | 98701.6 | 1 | Homo sapiens | ||
| 8 | S, T, W, X (b, Z, e, g) | Isoform 7 of DNA (cytosine-5)-methyltransferase 3B | polymer | 580 | 65568.4 | 4 | UniProt (Q9UBC3) Pfam (PF00145) Pfam (PF00855) Pfam (PF17980) Pfam (PF21255) | Homo sapiens (human) | Dnmt3b,DNA methyltransferase HsaIIIB,DNA MTase HsaIIIB,M.HsaIIIB |
| 9 | U, V, Y, Z (a, c, f, d) | DNA (cytosine-5)-methyltransferase 3A | polymer | 689 | 77914.7 | 4 | UniProt (Q9Y6K1) Pfam (PF00855) Pfam (PF17980) Pfam (PF21255) Pfam (PF00145) | Homo sapiens (human) | Dnmt3a,DNA methyltransferase HsaIIIA,M.HsaIIIA |
| 10 | AA, BA, CA, DA, EA... (b, a, c, e, f...) | ZINC ION | non-polymer | 65.4 | 18 | Chemie (ZN) PubChem (32051) | |||
| 11 | GA, KA, RA, VA (a, c, f, d) | S-ADENOSYL-L-HOMOCYSTEINE | non-polymer | 384.4 | 4 | Chemie (SAH) PubChem (439155) |
Sequence modifications
C, G, Y, S: 1 - 129 (UniProt: P06897)
D, H, P, T: 1 - 122 (UniProt: P02281)
E, W, Q: 1 - 135 (UniProt: P84233)
b, Z, e, g: 191 - 770 (UniProt: Q9UBC3)
| 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 |
|---|---|---|
| Ala 102 | Gly 103 | variant |
| PDB | External Database | Details |
|---|---|---|
| Lys 391 | - | insertion |
| Asp 392 | - | insertion |
| Tyr 393 | - | insertion |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 26 |
| Total formula weight | 989569.4 | |
| Non-Polymers* | Number of molecules | 22 |
| Total formula weight | 2715.0 | |
| All* | Total formula weight | 992284.4 |
