8JHO
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A, E, Q, U (A, E, a, e) | Histone H3 | polymer | 135 | 15332.0 | 4 | UniProt (A0A310TTQ1) Pfam (PF00125) UniProt (by SIFTS) (P84233) | Xenopus laevis (African clawed frog) | |
| 2 | B, F, R, V (B, F, b, f) | Histone H4 | polymer | 102 | 11263.2 | 4 | UniProt (A0A8J1LTD2) Pfam (PF15511) UniProt (by SIFTS) (P62799) | Xenopus laevis (African clawed frog) | |
| 3 | C, G, S, W (C, G, c, g) | Histone H2A | polymer | 129 | 13978.2 | 4 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) UniProt (by SIFTS) (P06897) | Xenopus laevis (African clawed frog) | |
| 4 | D, H, T, X (D, H, d, h) | Histone H2B | polymer | 122 | 13524.8 | 4 | UniProt (A0A8J0U496) Pfam (PF00125) UniProt (by SIFTS) (P02281) | Xenopus laevis (African clawed frog) | |
| 5 | I (I) | Di-nucleosome template foward | polymer | 350 | 107698.4 | 1 | synthetic construct | ||
| 6 | J (J) | Di-nucleosome template reverse | polymer | 350 | 108485.9 | 1 | synthetic construct | ||
| 7 | K (K) | Transcriptional regulatory protein SIN3 | polymer | 1536 | 175047.3 | 1 | UniProt (P22579) Pfam (PF16879) Pfam (PF02671) Pfam (PF08295) | Saccharomyces cerevisiae (baker's yeast) | |
| 8 | L (L) | Histone deacetylase RPD3 | polymer | 433 | 48962.0 | 1 | UniProt (P32561) Pfam (PF00850) | Saccharomyces cerevisiae (baker's yeast) | Transcriptional regulatory protein RPD3 |
| 9 | M, O (M, O) | Chromatin modification-related protein EAF3 | polymer | 401 | 45266.4 | 2 | UniProt (A0A8H4F719) Pfam (PF11717) Pfam (PF22732) Pfam (PF05712) UniProt (by SIFTS) (Q12432) | Saccharomyces cerevisiae (baker's yeast) | |
| 10 | N, P (N, P) | RCO1 isoform 1 | polymer | 684 | 78951.3 | 2 | UniProt (A0A8H4BXB0) Pfam (PF00628) UniProt (by SIFTS) (Q04779) | Saccharomyces cerevisiae (baker's yeast) | |
| 11 | AA, BA, CA, DA, EA... (N, P, L) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) |
Sequence modifications
A, E, a, e: 1 - 135 (UniProt: A0A310TTQ1)
| PDB | External Database | Details |
|---|---|---|
| Ala 110 | Cys 111 | engineered mutation |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 24 |
| Total formula weight | 905021.8 | |
| Non-Polymers* | Number of molecules | 7 |
| Total formula weight | 457.9 | |
| All* | Total formula weight | 905479.7 |
