6VYP
Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E, K, O (A, E, a, e) | Histone H3 | polymer | 135 | 15305.9 | 4 | UniProt (A0A310TTQ1) Pfam (PF00125) UniProt (by SIFTS) (P84233) | Xenopus laevis (African clawed frog) | |
| 2 | B, F, L, P (B, F, b, f) | Histone H4 | polymer | 102 | 11263.2 | 4 | UniProt (P62799) Pfam (PF15511) | Xenopus laevis (African clawed frog) | |
| 3 | C, G, M, Q (C, G, c, g) | Histone H2A type 1 | polymer | 129 | 13978.2 | 4 | UniProt (P06897) Pfam (PF00125) Pfam (PF16211) | Xenopus laevis (African clawed frog) | |
| 4 | D, H, N, R (D, H, d, h) | Histone H2B 1.1 | polymer | 122 | 13524.8 | 4 | UniProt (P02281) Pfam (PF00125) | Xenopus laevis (African clawed frog) | H2B1.1 |
| 5 | AA, I (I, i) | DNA (191-MER) | polymer | 191 | 58694.4 | 2 | synthetic construct | ||
| 6 | BA, J (J, j) | DNA (191-MER) | polymer | 191 | 59245.7 | 2 | synthetic construct | ||
| 7 | S, U, W, Y (M, m, K, k) | Lysine-specific histone demethylase 1A | polymer | 684 | 75732.6 | 4 | UniProt (O60341) Pfam (PF04433) Pfam (PF01593) | Homo sapiens (Human) | BRAF35-HDAC complex protein BHC110,Flavin-containing amine oxidase domain-containing protein 2 |
| 8 | T, V, X, Z (N, n, L, l) | REST corepressor 1 | polymer | 157 | 17956.4 | 4 | UniProt (Q9UKL0) Pfam (PF20878) Pfam (PF00249) | Homo sapiens (Human) | Protein CoREST |
| 9 | CA, DA, EA, FA (M, m, K, k) | FLAVIN-ADENINE DINUCLEOTIDE | non-polymer | 785.5 | 4 | Chemie (FAD) |
Sequence modifications
A, E, a, e: 1 - 135 (UniProt: A0A310TTQ1)
C, G, c, g: 1 - 129 (UniProt: P06897)
D, H, d, h: 1 - 122 (UniProt: P02281)
M, m, K, k: 171 - 852 (UniProt: O60341)
N, n, L, l: 286 - 440 (UniProt: Q9UKL0)
| PDB | External Database | Details |
|---|---|---|
| Met 4 | Lys 5 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Arg 99 | Gly 100 | engineered mutation |
| Ser 123 | Ala 124 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Thr 29 | Ser 33 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly 169 | - | expression tag |
| Ser 170 | - | expression tag |
| Ala 608 | Arg 608 | engineered mutation |
| Ala 717 | Asn 717 | engineered mutation |
| Ala 721 | Asp 721 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly 284 | - | expression tag |
| Ser 285 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 28 |
| Total formula weight | 826925.0 | |
| Non-Polymers* | Number of molecules | 4 |
| Total formula weight | 3142.2 | |
| All* | Total formula weight | 830067.2 |
