4IFD
Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Exosome complex component RRP45 | polymer | 304 | 33870.7 | 1 | UniProt (Q05636) Pfam (PF01138) Pfam (PF03725) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 45 |
| 2 | B (B) | Exosome complex component SKI6 | polymer | 248 | 27794.9 | 1 | UniProt (P46948) Pfam (PF01138) Pfam (PF03725) | Saccharomyces cerevisiae (Baker's yeast) | Extracellular mutant protein 20, Ribosomal RNA-processing protein 41, Superkiller protein 6 |
| 3 | C (C) | Exosome complex component RRP43 | polymer | 393 | 43977.8 | 1 | UniProt (P25359) Pfam (PF01138) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 43 |
| 4 | D (D) | Exosome complex component RRP46 | polymer | 245 | 26914.0 | 1 | UniProt (P53256) Pfam (PF01138) Pfam (PF03725) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 46 |
| 5 | E (E) | Exosome complex component RRP42 | polymer | 267 | 29294.4 | 1 | UniProt (Q12277) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 42 |
| 6 | F (F) | Exosome complex component MTR3 | polymer | 250 | 27559.9 | 1 | UniProt (P48240) Pfam (PF01138) | Saccharomyces cerevisiae (Baker's yeast) | mRNA transport regulator 3 |
| 7 | G (G) | Exosome complex component RRP40 | polymer | 242 | 26778.6 | 1 | UniProt (Q08285) Pfam (PF21262) Pfam (PF15985) Pfam (PF18311) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 40 |
| 8 | H (H) | Exosome complex component RRP4 | polymer | 361 | 39714.4 | 1 | UniProt (P38792) Pfam (PF14382) Pfam (PF21266) Pfam (PF15985) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 4 |
| 9 | I (I) | Exosome complex component CSL4 | polymer | 301 | 32805.6 | 1 | UniProt (P53859) Pfam (PF21551) Pfam (PF10447) | Saccharomyces cerevisiae (Baker's yeast) | CEP1 synthetic lethal protein 4 |
| 10 | J (J) | Exosome complex exonuclease DIS3 | polymer | 1003 | 113983.9 | 1 | UniProt (Q08162) Pfam (PF13638) Pfam (PF17216) Pfam (PF17849) Pfam (PF00773) Pfam (PF17215) | Saccharomyces cerevisiae (Baker's yeast) | Chromosome disjunction protein 3, Ribosomal RNA-processing protein 44 |
| 11 | K (K) | Exosome complex exonuclease RRP6 | polymer | 179 | 19876.9 | 1 | UniProt (Q12149) | Saccharomyces cerevisiae (Baker's yeast) | Ribosomal RNA-processing protein 6 |
| 12 | L (R) | RNA (45-MER) | polymer | 45 | 14046.9 | 1 | |||
| 13 | AA, BA, M, N, P... (J, A, E, F, H...) | BROMIDE ION | non-polymer | 79.9 | 10 | Chemie (BR) | |||
| 14 | O, R, U, V, W (C, G, H) | GLYCEROL | non-polymer | 92.1 | 5 | Chemie (GOL) | |||
| 15 | S (G) | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID | non-polymer | 195.2 | 1 | Chemie (MES) | |||
| 16 | CA (J) | MAGNESIUM ION | non-polymer | 24.3 | 1 | Chemie (MG) | |||
| 17 | DA (J) | ZINC ION | non-polymer | 65.4 | 1 | Chemie (ZN) | |||
| 18 | EA, FA, GA, HA, IA... (A, B, C, D, E...) | water | water | 18.0 | 244 | Chemie (HOH) |
Sequence modifications
B: 1 - 246 (UniProt: P46948)
C: 2 - 394 (UniProt: P25359)
D: 1 - 223 (UniProt: P53256)
E: 1 - 265 (UniProt: Q12277)
F: 1 - 250 (UniProt: P48240)
G: 1 - 240 (UniProt: Q08285)
H: 1 - 359 (UniProt: P38792)
I: 1 - 292 (UniProt: P53859)
J: 1 - 1001 (UniProt: Q08162)
K: 518 - 693 (UniProt: Q12149)
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| His 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Ser 102 | Ala 102 | engineered mutation |
| Met 363 | Val 363 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly -21 | - | expression tag |
| His -20 | - | expression tag |
| Gly -19 | - | expression tag |
| Asn -18 | - | expression tag |
| Asn -17 | - | expression tag |
| Lys -16 | - | expression tag |
| Glu -15 | - | expression tag |
| Pro -14 | - | expression tag |
| Asn -13 | - | expression tag |
| Thr -12 | - | expression tag |
| Lys -11 | - | expression tag |
| Asn -10 | - | expression tag |
| Arg -9 | - | expression tag |
| Leu -8 | - | expression tag |
| Asp -7 | - | expression tag |
| Ser -6 | - | expression tag |
| Ala -5 | - | expression tag |
| Glu -4 | - | expression tag |
| Lys -3 | - | expression tag |
| Lys -2 | - | expression tag |
| Lys -1 | - | expression tag |
| Lys 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| His 0 | - | expression tag |
| Ile 138 | Val 138 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Ser 75 | Thr 75 | engineered mutation |
| Thr 161 | Met 161 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| His 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Arg -1 | - | expression tag |
| Ser 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Met -8 | - | expression tag |
| Lys -7 | - | expression tag |
| His -6 | - | expression tag |
| His -5 | - | expression tag |
| His -4 | - | expression tag |
| His -3 | - | expression tag |
| His -2 | - | expression tag |
| His -1 | - | expression tag |
| Pro 0 | - | expression tag |
| PDB | External Database | Details |
|---|---|---|
| Gly -1 | - | expression tag |
| Ala 0 | - | expression tag |
| Asn 171 | Asp 171 | engineered mutation |
| Asn 551 | Asp 551 | engineered mutation |
| PDB | External Database | Details |
|---|---|---|
| Arg 515 | - | expression tag |
| Ser 516 | - | expression tag |
| Met 517 | - | expression tag |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 12 |
| Total formula weight | 436618.0 | |
| Non-Polymers* | Number of molecules | 18 |
| Total formula weight | 1544.5 | |
| All* | Total formula weight | 438162.5 |
