8HXY
Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with 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 | Histone H3 | polymer | 135 | 15332.0 | 2 | UniProt (A0A310TTQ1) Pfam (PF00125) UniProt (by SIFTS) (P84233) In PDB | Xenopus laevis (African clawed frog) | |
| 2 | B, F | Histone H4 | polymer | 102 | 11263.2 | 2 | UniProt (A0A8J1LTD2) Pfam (PF15511) UniProt (by SIFTS) (P62799) In PDB | Xenopus laevis (African clawed frog) | |
| 3 | C, G | Histone H2A | polymer | 129 | 13978.2 | 2 | UniProt (Q6AZJ8) Pfam (PF00125) Pfam (PF16211) UniProt (by SIFTS) (P06897) In PDB | Xenopus laevis (African clawed frog) | |
| 4 | D, H | Histone H2B | polymer | 122 | 13524.8 | 2 | UniProt (A0A8J0U496) Pfam (PF00125) UniProt (by SIFTS) (P02281) In PDB | Xenopus laevis (African clawed frog) | |
| 5 | I | DNA (352-MER) | polymer | 352 | 108340.8 | 1 | synthetic construct | ||
| 6 | J | DNA (352-MER) | polymer | 352 | 109079.3 | 1 | synthetic construct | ||
| 7 | K | Transcriptional regulatory protein SIN3 | polymer | 1536 | 175047.3 | 1 | UniProt (P22579) Pfam (PF16879) Pfam (PF02671) Pfam (PF08295) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 8 | L | Histone deacetylase RPD3 | polymer | 433 | 48962.0 | 1 | UniProt (P32561) Pfam (PF00850) In PDB | Saccharomyces cerevisiae (baker's yeast) | Transcriptional regulatory protein RPD3 |
| 9 | M | Chromatin modification-related protein EAF3 | polymer | 401 | 45266.4 | 1 | UniProt (A0A8H4F719) Pfam (PF11717) Pfam (PF22732) Pfam (PF05712) UniProt (by SIFTS) (Q12432) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 10 | N, P | Transcriptional regulatory protein RCO1 | polymer | 684 | 78951.3 | 2 | UniProt (A0A8H4BXB0) Pfam (PF00628) UniProt (by SIFTS) (Q04779) In PDB | Saccharomyces cerevisiae (baker's yeast) | |
| 11 | L, N | ZINC ION | non-polymer | 65.4 | 5 | Chemie (ZN) |
Sequence modifications
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 | 15 |
| Total formula weight | 752794.8 | |
| Non-Polymers* | Number of molecules | 5 |
| Total formula weight | 327.0 | |
| All* | Total formula weight | 753121.8 |
