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 (PF23240) Pfam (PF02184) Pfam (PF23231) | 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 (PF23231) | 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) PubChem (136073927) PubChem (135398619) PubChem (135402030) PubChem (135431654) PubChem (135566337) PubChem (135760556) PubChem (136026707) PubChem (136053418) PubChem (136663964) PubChem (136664748) PubChem (136759848) PubChem (136759849) PubChem (136759850) PubChem (136836636) PubChem (136847074) PubChem (172898537) | |||
| 35 | SA, TA, UA, VA (N) | MAGNESIUM ION | non-polymer | 24.3 | 4 | Chemie (MG) PubChem (888) | |||
| 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 |
