5GM6
Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution
This is a non-PDB format compatible entry.
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 | 2287 | 265949.2 | 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) | Pre-mRNA-splicing helicase BRR2 | polymer | 2163 | 246470.3 | 1 | UniProt (P32639) Pfam (PF00270) Pfam (PF00271) Pfam (PF02889) Pfam (PF21188) Pfam (PF18149) | Saccharomyces cerevisiae (Baker's yeast) | Protein Snu246 |
| 3 | C (C) | Pre-mRNA-splicing factor SNU114 | polymer | 1008 | 114174.0 | 1 | UniProt (P36048) Pfam (PF16004) Pfam (PF00009) Pfam (PF03764) Pfam (PF00679) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | 114 kDa U5 small nuclear ribonucleoprotein component,Growth inhibitory protein 10 |
| 4 | D (D) | Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence | polymer | 214 | 68643.3 | 1 | GenBank (1039023403) | Saccharomyces cerevisiae | |
| 5 | E (E) | Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence | polymer | 112 | 35883.2 | 1 | GenBank (1039022925) | Saccharomyces cerevisiae | |
| 6 | F (F) | Pre-mRNA-splicing factor RSE1 | polymer | 1361 | 153956.8 | 1 | UniProt (Q04693) Pfam (PF10433) Pfam (PF03178) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | RNA splicing and ER to Golgi transport factor 1,Spliceosome-associated protein 130 |
| 7 | G (H) | Cold sensitive U2 snRNA suppressor 1 | polymer | 436 | 50339.9 | 1 | UniProt (Q02554) Pfam (PF04037) Pfam (PF04046) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 8 | H (I) | Pre-mRNA-splicing factor PRP11 | polymer | 266 | 29962.8 | 1 | UniProt (Q07350) Pfam (PF12874) Pfam (PF16835) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 9 | I (J) | Pre-mRNA-splicing factor RDS3 | polymer | 107 | 12283.6 | 1 | UniProt (Q06835) Pfam (PF03660) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Regulator of drug sensitivity 3 |
| 10 | J (K) | RDS3 complex subunit 10 | polymer | 85 | 10045.4 | 1 | UniProt (P0C074) Pfam (PF07189) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Splicing factor 3b subunit |
| 11 | K (L) | U2 snRNA | polymer | 1175 | 376267.4 | 1 | Saccharomyces cerevisiae S288c | ||
| 12 | L (N) | Pre-mRNA | polymer | 25 | 7864.5 | 1 | Saccharomyces cerevisiae S288c | ||
| 13 | M (M) | Pre-mRNA | polymer | 61 | 18915.3 | 1 | Saccharomyces cerevisiae S288c | ||
| 14 | N (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 |
| 15 | O (P) | Pre-mRNA-processing protein 45 | polymer | 379 | 42548.7 | 1 | UniProt (P28004) Pfam (PF02731) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 16 | P (Q) | 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 |
| 17 | Q (R) | 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 |
| 18 | R (S) | 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 |
| 19 | S (T) | 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 |
| 20 | T (U) | Pre-mRNA leakage protein 1 | polymer | 207 | 24100.1 | 1 | UniProt (Q07930) Pfam (PF00498) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 21 | U (V) | U2 snRNP component IST3 | polymer | 148 | 17121.1 | 1 | UniProt (P40565) Pfam (PF00076) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Increased sodium tolerance protein 3,U2 snRNP protein SNU17 |
| 22 | V (W) | Pre-mRNA-splicing factor CWC26 | polymer | 266 | 30529.1 | 1 | UniProt (P46947) Pfam (PF09736) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Bud site selection protein 13,Complexed with CEF1 protein 26 |
| 23 | W (Y) | Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 | polymer | 876 | 99947.5 | 1 | UniProt (P20095) Pfam (PF00270) Pfam (PF00271) Pfam (PF04408) Pfam (PF21010) Pfam (PF07717) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Pre-mRNA-processing protein 2 |
| 24 | X (Z) | Pre-mRNA-splicing factor CWC22 | polymer | 577 | 67386.1 | 1 | UniProt (P53333) Pfam (PF02847) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 22 |
| 25 | Y (a) | Pre-mRNA-splicing factor CWC24 | polymer | 259 | 29797.9 | 1 | UniProt (P53769) Pfam (PF00642) Pfam (PF13923) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 24 |
| 26 | Z (b) | Peptidyl-prolyl isomerase CWC27 | polymer | 301 | 35080.9 | 1 | UniProt (Q02770) Pfam (PF00160) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PPIase CWC27,Complexed with CEF1 protein 27,Rotamase CWC27 |
| 27 | AA (c) | Pre-mRNA-splicing factor CEF1 | polymer | 587 | 61057.6 | 1 | UniProt (Q03654) Pfam (PF00249) Pfam (PF11831) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | PRP nineteen-associated complex protein 85 |
| 28 | BA (G) | U2 snRNP component HSH155 | polymer | 971 | 110166.7 | 1 | UniProt (P49955) Pfam (PF22646) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 29 | CA (d) | Pre-mRNA-splicing factor CLF1 | polymer | 687 | 68044.6 | 1 | UniProt (Q12309) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Crooked neck-like factor 1,PRP19-associated complex protein 77 |
| 30 | DA (X) | Pre-mRNA-splicing factor CWC21 | polymer | 135 | 15793.6 | 1 | UniProt (Q03375) Pfam (PF08312) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Complexed with CEF1 protein 21 |
| 31 | EA (v) | Pre-mRNA-splicing factor SYF1 | polymer | 859 | 78125.6 | 1 | UniProt (Q04048) | Saccharomyces cerevisiae S288c | PRP19-associated complex protein 90s,Synthetic lethal with CDC40 protein 1 |
| 32 | FA (e) | Protein HSH49 | polymer | 213 | 24534.2 | 1 | UniProt (Q99181) Pfam (PF00076) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 33 | GA (f) | 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 |
| 34 | HA, IA, JA, KA (o, p, q, r) | Pre-mRNA-processing factor 19 | polymer | 503 | 56629.8 | 4 | UniProt (P32523) Pfam (PF08606) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | |
| 35 | LA (t) | 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 |
| 36 | MA (n) | 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 |
| 37 | NA (k) | Small nuclear ribonucleoprotein-associated protein B | polymer | 196 | 22427.0 | 1 | UniProt (P40018) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-B,Sm protein B,SmB |
| 38 | OA (i) | Small nuclear ribonucleoprotein E | polymer | 94 | 10385.1 | 1 | UniProt (Q12330) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-E,Sm protein E,SmE |
| 39 | PA (h) | Small nuclear ribonucleoprotein F | polymer | 86 | 9669.9 | 1 | UniProt (P54999) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-F,Sm protein F,SmF |
| 40 | QA (j) | Small nuclear ribonucleoprotein G | polymer | 77 | 8490.8 | 1 | UniProt (P40204) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | snRNP-G,Sm protein G,SmG |
| 41 | RA (l) | Small nuclear ribonucleoprotein Sm D3 | polymer | 101 | 11240.1 | 1 | UniProt (P43321) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D3,snRNP core protein D3 |
| 42 | SA (m) | Small nuclear ribonucleoprotein Sm D1 | polymer | 146 | 16296.8 | 1 | UniProt (Q02260) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D1,snRNP core protein D1 |
| 43 | TA (g) | Small nuclear ribonucleoprotein Sm D2 | polymer | 94 | 11022.0 | 1 | UniProt (Q06217) Pfam (PF01423) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) | Sm-D2,snRNP core protein D2 |
| 44 | UA (C) | GUANOSINE-5'-TRIPHOSPHATE | non-polymer | 523.2 | 1 | Chemie (GTP) | |||
| 45 | JB, VA, WA, XA, YA (Y, E) | MAGNESIUM ION | non-polymer | 24.3 | 5 | Chemie (MG) | |||
| 46 | AB, BB, CB, DB, EB... (J, Q, R, T, a...) | ZINC ION | non-polymer | 65.4 | 13 | Chemie (ZN) | |||
| 47 | KB (Y) | ADENOSINE-5'-DIPHOSPHATE | non-polymer | 427.2 | 1 | Chemie (ADP) |
Sequence modifications
A: 128 - 2413 (UniProt: P33334)
U: 1 - 204 (UniProt: Q07930)
c: 1 - 253 (UniProt: Q03654)
c: 254 - 481 (PDB: 5GM6)
c: 482 - 587 (UniProt: Q03654)
d: 1 - 275 (UniProt: Q12309)
d: 276 - 687 (PDB: 5GM6)
v: 1 - 568 (PDB: 5GM6)
v: 569 - 734 (UniProt: Q04048)
v: 735 - 859 (PDB: 5GM6)
| PDB | External Database | Details |
|---|---|---|
| Ala 127 | - | insertion |
| PDB | External Database | Details |
|---|---|---|
| His 205 | - | insertion |
| His 206 | - | insertion |
| His 207 | - | insertion |
c: 254 - 481 (PDB: 5GM6)
c: 482 - 587 (UniProt: Q03654)
d: 1 - 275 (UniProt: Q12309)
d: 276 - 687 (PDB: 5GM6)
v: 1 - 568 (PDB: 5GM6)
v: 569 - 734 (UniProt: Q04048)
v: 735 - 859 (PDB: 5GM6)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 46 |
| Total formula weight | 2677467.2 | |
| Non-Polymers* | Number of molecules | 20 |
| Total formula weight | 1922.2 | |
| All* | Total formula weight | 2679389.5 |
