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 (PF23445) 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 (PF23726) 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) Pfam (PF23233) | 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) Pfam (PF23231) | 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) PubChem (177679032) PubChem (135400627) PubChem (135487750) PubChem (136088935) PubChem (136803486) PubChem (135398633) PubChem (135544356) PubChem (135547949) PubChem (135600366) PubChem (135749822) PubChem (136005188) PubChem (136073923) PubChem (136240914) PubChem (136664747) PubChem (136772743) PubChem (136772744) PubChem (136803487) PubChem (137286749) PubChem (164715984) PubChem (171699466) | |||
| 45 | JB, VA, WA, XA, YA (Y, E) | MAGNESIUM ION | non-polymer | 24.3 | 5 | Chemie (MG) PubChem (888) | |||
| 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 |
