5Y88
Cryo-EM structure of the intron-lariat spliceosome ready for disassembly from S.cerevisiae at 3.5 angstrom
Entity
| Entity ID | Chain ID | Description | Type | Chain length | Formula weight | Number of molecules | DB Name (Accession) | Biological source | Descriptive keywords |
| 1 | A (A) | Pre-mRNA-splicing factor 8 | polymer | 2413 | 279867.5 | 1 | UniProt (P33334) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF08084) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 2 | B (B) | U5 snRNA | polymer | 214 | 68643.3 | 1 | Saccharomyces cerevisiae S288c (Baker's yeast) | ||
| 3 | C (C) | Pre-mRNA-splicing factor SNU114 | polymer | 1008 | 114174.0 | 1 | UniProt (P36048) Pfam (PF03764) Pfam (PF00679) Pfam (PF16004) Pfam (PF00009) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | 114 kDa U5 small nuclear ribonucleoprotein component,Growth inhibitory protein 10 |
| 4 | D (D) | U6 snRNA | polymer | 112 | 35883.2 | 1 | GenBank (1039023367) | Saccharomyces cerevisiae S288c (Baker's yeast) | |
| 5 | E (E) | Intron lariat | polymer | 38 | 10810.2 | 1 | Saccharomyces cerevisiae S288c (Baker's yeast) | ||
| 6 | F (F) | U2 snRNA | polymer | 1175 | 376267.4 | 1 | Saccharomyces cerevisiae S288c (Baker's yeast) | ||
| 7 | G (G) | Pre-mRNA-splicing factor SNT309 | polymer | 175 | 20741.5 | 1 | UniProt (Q06091) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PRP19-associated complex protein 25,Synergistic to PRP19 mutation protein 309 |
| 8 | H (H) | Pre-mRNA-splicing factor SYF1 | polymer | 859 | 100344.0 | 1 | UniProt (Q04048) Pfam (PF23233) Pfam (PF23220) Pfam (PF23231) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PRP19-associated complex protein 90,Synthetic lethal with CDC40 protein 1 |
| 9 | I (I) | Pre-mRNA-splicing factor CLF1 | polymer | 687 | 82555.9 | 1 | UniProt (Q12309) Pfam (PF23233) Pfam (PF23240) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Crooked neck-like factor 1,PRP19-associated complex protein 77,Synthetic lethal with CDC40 protein 3 |
| 10 | J (J) | Pre-mRNA-splicing factor CEF1 | polymer | 590 | 67837.8 | 1 | UniProt (Q03654) Pfam (PF00249) Pfam (PF11831) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PRP nineteen-associated complex protein 85,PRP19-associated complex protein 85 |
| 11 | K (K) | Pre-mRNA-splicing factor SYF2 | polymer | 215 | 24850.7 | 1 | UniProt (P53277) Pfam (PF08231) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PRP19 complex protein 31,Synthetic lethal with CDC40 protein 2 |
| 12 | L (L) | Pre-mRNA-splicing factor BUD31 | polymer | 157 | 18484.5 | 1 | UniProt (P25337) Pfam (PF01125) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Bud site selection protein 31,Complexed with CEF1 protein 14 |
| 13 | M (M) | Pre-mRNA-splicing factor SLT11 | polymer | 364 | 40988.6 | 1 | UniProt (P38241) Pfam (PF21369) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Extracellular mutant protein 2,Synthetic lethality with U2 protein 11 |
| 14 | N (N) | Pre-mRNA-splicing factor CWC2 | polymer | 339 | 38486.6 | 1 | UniProt (Q12046) Pfam (PF16131) Pfam (PF00076) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 2,PRP19-associated complex protein 40,Synthetic lethal with CLF1 protein 3 |
| 15 | O (O) | Pre-mRNA-splicing factor PRP46 | polymer | 451 | 50771.3 | 1 | UniProt (Q12417) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 1,PRP nineteen-associated complex protein 50,PRP19-associated complex protein 50,Pre-mRNA-processing protein 46 |
| 16 | P (P) | Pre-mRNA-splicing factor CWC15 | polymer | 175 | 19975.2 | 1 | UniProt (Q03772) Pfam (PF04889) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 15 |
| 17 | Q (Q) | Pre-mRNA-processing protein 45 | polymer | 379 | 42548.7 | 1 | UniProt (P28004) Pfam (PF02731) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 18 | R (R) | Protein CWC16 | polymer | 278 | 32371.1 | 1 | UniProt (P28320) Pfam (PF04502) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 19 | S (S) | Pre-mRNA-processing factor 17 | polymer | 455 | 52128.8 | 1 | UniProt (P40968) Pfam (PF00400) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Cell division control protein 40 |
| 20 | T (T) | Pre-mRNA-splicing factor CWC23 | polymer | 283 | 33280.4 | 1 | UniProt (P52868) Pfam (PF00226) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 23 |
| 21 | U (U) | Pre-mRNA-splicing factor SPP382 | polymer | 708 | 83155.5 | 1 | UniProt (Q06411) Pfam (PF01585) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | CLF1 complex factor 8,Nineteen complex-related protein 1,NTC-related protein 1,Suppressor of PRP38 protein 2 |
| 22 | V (V) | Pre-mRNA-splicing factor NTR2 | polymer | 322 | 36705.4 | 1 | UniProt (P36118) Pfam (PF15458) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Nineteen complex-related protein 2,NTC-related protein 2 |
| 23 | W (W) | Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 | polymer | 767 | 87682.8 | 1 | UniProt (P53131) Pfam (PF00270) Pfam (PF00271) Pfam (PF04408) Pfam (PF21010) Pfam (PF07717) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Helicase JA1 |
| 24 | GA, X (a, h) | Small nuclear ribonucleoprotein-associated protein B | polymer | 196 | 22427.0 | 2 | UniProt (P40018) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-B,Sm protein B,SmB |
| 25 | HA, Y (b, i) | Small nuclear ribonucleoprotein E | polymer | 94 | 10385.1 | 2 | UniProt (Q12330) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-E,Sm protein E,SmE |
| 26 | IA, Z (c, j) | Small nuclear ribonucleoprotein F | polymer | 86 | 9669.9 | 2 | UniProt (P54999) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-F,Sm protein F,SmF |
| 27 | AA, JA (d, k) | Small nuclear ribonucleoprotein G | polymer | 77 | 8490.8 | 2 | UniProt (P40204) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-G,Sm protein G,SmG |
| 28 | BA, KA (e, l) | Small nuclear ribonucleoprotein Sm D3 | polymer | 101 | 11240.1 | 2 | UniProt (P43321) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D3,snRNP core protein D3 |
| 29 | CA, LA (f, m) | Small nuclear ribonucleoprotein Sm D1 | polymer | 146 | 16296.8 | 2 | UniProt (Q02260) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D1,snRNP core protein D1 |
| 30 | DA, MA (g, n) | Small nuclear ribonucleoprotein Sm D2 | polymer | 110 | 12876.1 | 2 | UniProt (Q06217) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D2,snRNP core protein D2 |
| 31 | EA (o) | U2 small nuclear ribonucleoprotein A' | polymer | 238 | 27232.3 | 1 | UniProt (Q08963) Pfam (PF14580) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U2 snRNP A',Looks exceptionally like U2A protein 1 |
| 32 | FA (p) | U2 small nuclear ribonucleoprotein B'' | polymer | 111 | 12850.9 | 1 | UniProt (P40567) Pfam (PF13893) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | U2 snRNP B'' |
| 33 | NA, OA, PA, QA (q, r, s, t) | Pre-mRNA-processing factor 19 | polymer | 503 | 56629.8 | 4 | UniProt (P32523) Pfam (PF08606) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RING-type E3 ubiquitin transferase PRP19 |
| 34 | RA (x) | RNA (intron or U6 snRNA) | polymer | 9 | 2710.5 | 1 | Saccharomyces cerevisiae S288c (Baker's yeast) | ||
| 35 | SA (A) | INOSITOL HEXAKISPHOSPHATE | non-polymer | 660.0 | 1 | Chemie (IHP) | |||
| 36 | TA (C) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 37 | UA, VA, WA, XA, YA... (C, D) | MAGNESIUM ION | non-polymer | 24.3 | 6 | Chemie (MG) | |||
| 38 | AB, BB, CB, DB, EB... (L, M, N) | ZINC ION | non-polymer | 65.4 | 6 | Chemie (ZN) |
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 44 |
| Total formula weight | 2170638.6 | |
| Non-Polymers* | Number of molecules | 14 |
| Total formula weight | 1721.5 | |
| All* | Total formula weight | 2172360.1 |
