3JB9
Cryo-EM structure of the yeast spliceosome at 3.6 angstrom resolution
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 spp42 | polymer | 2363 | 274917.8 | 1 | UniProt (O14187) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF01398) Pfam (PF08084) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 6 |
| 2 | B (B) | Pre-mRNA-splicing factor cwf10 | polymer | 984 | 111445.3 | 1 | UniProt (O94316) Pfam (PF00009) Pfam (PF03144) Pfam (PF03764) Pfam (PF00679) Pfam (PF16004) | Schizosaccharomyces pombe 972h- (Fission yeast) | 114 kDa U5 small nuclear ribonucleoprotein component homolog, Complexed with cdc5 protein 10 |
| 3 | C (C) | U5 snRNA | polymer | 120 | 38191.4 | 1 | Schizosaccharomyces pombe (Fission yeast) | ||
| 4 | D, JA (D, Z) | Small nuclear ribonucleoprotein Sm D3 | polymer | 97 | 11050.9 | 2 | UniProt (Q9UUC6) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | Sm-D3, snRNP core protein D3 |
| 5 | E, KA (E, b) | Small nuclear ribonucleoprotein-associated protein B | polymer | 147 | 15493.0 | 2 | UniProt (Q10163) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | snRNP-B, Sm protein B, Sm-B, SmB |
| 6 | F, LA (F, f) | Small nuclear ribonucleoprotein Sm D1 | polymer | 117 | 13115.4 | 2 | UniProt (O42661) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | Sm-D1, snRNP core protein D1 |
| 7 | G, MA (G, l) | Small nuclear ribonucleoprotein Sm D2 | polymer | 115 | 13119.3 | 2 | UniProt (O14036) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | Sm-D2, Complexed with cdc5 protein 9, snRNP core protein D2 |
| 8 | H, NA (H, m) | Small nuclear ribonucleoprotein E | polymer | 84 | 9702.4 | 2 | UniProt (Q9USZ3) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | snRNP-E, Sm protein E, Sm-E, SmE |
| 9 | I, OA (I, n) | Small nuclear ribonucleoprotein F | polymer | 78 | 8667.1 | 2 | UniProt (O59734) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | snRNP-F, Sm protein F, Sm-F, SmF |
| 10 | J, PA (J, o) | Small nuclear ribonucleoprotein G | polymer | 77 | 8616.0 | 2 | UniProt (O74966) Pfam (PF01423) | Schizosaccharomyces pombe 972h- (Fission yeast) | snRNP-G, Sm protein G, Sm-G, SmG |
| 11 | K (K) | Pre-mRNA-splicing factor prp5 | polymer | 473 | 48909.7 | 1 | UniProt (O13615) Pfam (PF00400) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 1, Pre-mRNA-processing protein 5 |
| 12 | L (L) | Pre-mRNA-splicing factor cwf17 | polymer | 340 | 37477.2 | 1 | UniProt (O94620) Pfam (PF00400) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 17 |
| 13 | M (M) | Pre-mRNA-processing protein 45 | polymer | 557 | 62798.2 | 1 | UniProt (Q09882) Pfam (PF02731) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 13, Transcriptional coregulator snw1 |
| 14 | N (N) | U6 snRNA | polymer | 99 | 31864.0 | 1 | Schizosaccharomyces pombe (Fission yeast) | ||
| 15 | O (O) | RNA (5'-R(P*GP*UP*AP*UP*GP*UP*AP*U)-3') | polymer | 8 | 2528.5 | 1 | Schizosaccharomyces pombe (Fission yeast) | ||
| 16 | P (Q) | RNA (5'-R(P*UP*UP*UP*AP*UP*AP*CP*UP*AP*AP*CP*AP*C)-3') | polymer | 13 | 4047.4 | 1 | Schizosaccharomyces pombe (Fission yeast) | ||
| 17 | Q (P) | U2 snRNA | polymer | 186 | 59207.5 | 1 | Schizosaccharomyces pombe (Fission yeast) | ||
| 18 | R, S, T, U (S, T, U, V) | Pre-mRNA-processing factor 19 | polymer | 488 | 54244.0 | 4 | UniProt (O14011) Pfam (PF08606) Pfam (PF00400) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 8 |
| 19 | V (W) | Pre-mRNA-splicing factor cdc5 | polymer | 757 | 75128.1 | 1 | UniProt (P39964) Pfam (PF00249) Pfam (PF11831) | Schizosaccharomyces pombe 972h- (Fission yeast) | Cell division control protein 5 |
| 20 | W (Y) | Pre-mRNA-splicing factor cwf2 | polymer | 388 | 41838.9 | 1 | UniProt (P87126) Pfam (PF16131) Pfam (PF00076) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 2, Pre-mRNA-processing protein 3 |
| 21 | X (a) | Pre-mRNA-splicing factor cwf5 | polymer | 354 | 37133.5 | 1 | UniProt (O59800) Pfam (PF21369) Pfam (PF00076) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 5 |
| 22 | Y (c) | Pre-mRNA-splicing factor cwf19 | polymer | 639 | 74547.5 | 1 | UniProt (Q09909) Pfam (PF04677) Pfam (PF04676) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 19 |
| 23 | Z (d) | Peptidyl-prolyl cis-trans isomerase ppi1 | polymer | 155 | 16884.2 | 1 | UniProt (P87051) Pfam (PF00160) | Schizosaccharomyces pombe 972h- (Fission yeast) | PPIase ppi1, Cyclophilin ppi1, Rotamase ppi1 |
| 24 | AA (e) | Pre-mRNA-splicing factor cwf14 | polymer | 146 | 17122.8 | 1 | UniProt (O74772) Pfam (PF01125) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 14 |
| 25 | BA (g) | Pre-mRNA-processing factor 17 | polymer | 558 | 63211.3 | 1 | UniProt (O43071) Pfam (PF00400) | Schizosaccharomyces pombe 972h- (Fission yeast) | |
| 26 | CA (h) | Pre-mRNA-splicing factor cwf15 | polymer | 265 | 30479.0 | 1 | UniProt (P78794) Pfam (PF04889) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 15 |
| 27 | DA (i) | Pre-mRNA-splicing factor cwf7 | polymer | 187 | 21348.2 | 1 | UniProt (Q9USV3) Pfam (PF05700) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 7, Splicing factor 27 |
| 28 | EA (R) | Pre-mRNA-splicing factor cwf4 | polymer | 674 | 67082.7 | 1 | UniProt (P87312) Pfam (PF05843) Pfam (PF02184) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 4 |
| 29 | FA (r) | Pre-mRNA-splicing factor cwf3 | polymer | 790 | 72172.1 | 1 | UniProt (Q9P7R9) Pfam (PF05843) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 3 |
| 30 | GA (X) | Pre-mRNA-splicing factor cwf11 | polymer | 1284 | 148532.9 | 1 | UniProt (O94508) Pfam (PF16399) Pfam (PF13087) | Schizosaccharomyces pombe 972h- (Fission yeast) | Complexed with cdc5 protein 11 |
| 31 | HA (j) | U2 small nuclear ribonucleoprotein A' | polymer | 239 | 27260.4 | 1 | UniProt (Q9USX8) Pfam (PF12799) | Schizosaccharomyces pombe 972h- (Fission yeast) | U2 snRNP A' |
| 32 | IA (k) | Probable U2 small nuclear ribonucleoprotein B'' | polymer | 111 | 12685.7 | 1 | UniProt (Q7LL14) Pfam (PF00076) | Schizosaccharomyces pombe 972h- (Fission yeast) | U2 snRNP B'' |
| 33 | QA (x) | unknown chain | polymer | 412 | 35081.2 | 1 | Schizosaccharomyces pombe 972h- (Fission yeast) | ||
| 34 | RA (B) | GUANOSINE-5'-DIPHOSPHATE | non-polymer | 443.2 | 1 | Chemie (GDP) | |||
| 35 | SA, TA, UA, VA (N) | MAGNESIUM ION | non-polymer | 24.3 | 4 | Chemie (MG) | |||
| 36 | AB, BB, CB, WA, XA... (e, Y, a, c) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) | |||
| 37 | DB (X) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) |
Sequence modifications
K: 1 - 148 (PDB: 3JB9)
K: 149 - 473 (UniProt: O13615)
W: 1 - 236 (UniProt: P39964)
W: 237 - 651 (PDB: 3JB9)
W: 652 - 757 (UniProt: P39964)
Y: 1 - 289 (UniProt: P87126)
Y: 290 - 388 (PDB: 3JB9)
a: 1 - 151 (UniProt: O59800)
a: 152 - 177 (PDB: 3JB9)
a: 178 - 285 (UniProt: O59800)
a: 286 - 354 (PDB: 3JB9)
R: 1 - 40 (PDB: 3JB9)
R: 41 - 290 (UniProt: P87312)
R: 291 - 674 (PDB: 3JB9)
r: 1 - 497 (PDB: 3JB9)
r: 498 - 653 (UniProt: Q9P7R9)
r: 654 - 790 (PDB: 3JB9)
K: 149 - 473 (UniProt: O13615)
W: 1 - 236 (UniProt: P39964)
W: 237 - 651 (PDB: 3JB9)
W: 652 - 757 (UniProt: P39964)
Y: 1 - 289 (UniProt: P87126)
Y: 290 - 388 (PDB: 3JB9)
a: 1 - 151 (UniProt: O59800)
a: 152 - 177 (PDB: 3JB9)
a: 178 - 285 (UniProt: O59800)
a: 286 - 354 (PDB: 3JB9)
R: 1 - 40 (PDB: 3JB9)
R: 41 - 290 (UniProt: P87312)
R: 291 - 674 (PDB: 3JB9)
r: 1 - 497 (PDB: 3JB9)
r: 498 - 653 (UniProt: Q9P7R9)
r: 654 - 790 (PDB: 3JB9)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 43 |
| Total formula weight | 1788399.6 | |
| Non-Polymers* | Number of molecules | 13 |
| Total formula weight | 1425.5 | |
| All* | Total formula weight | 1789825.1 |
