5GMK
Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 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 8 | polymer | 2413 | 279867.5 | 1 | UniProt (P33334) Pfam (PF08082) Pfam (PF08083) Pfam (PF10598) Pfam (PF10597) Pfam (PF10596) Pfam (PF12134) Pfam (PF08084) | Saccharomyces cerevisiae S288C | |
| 2 | B (C) | Pre-mRNA-splicing factor SNU114 | polymer | 1008 | 114174.0 | 1 | UniProt (P36048) Pfam (PF03764) Pfam (PF00679) Pfam (PF16004) Pfam (PF00009) | Saccharomyces cerevisiae S288C | 114 kDa U5 small nuclear ribonucleoprotein component |
| 3 | C (D) | U5 snRNA | polymer | 214 | 68643.3 | 1 | Saccharomyces cerevisiae S288c | ||
| 4 | D (E) | U6 snRNA | polymer | 112 | 35883.2 | 1 | Saccharomyces cerevisiae S288c | ||
| 5 | E (L) | U2 snRNA | polymer | 1175 | 376267.4 | 1 | Saccharomyces cerevisiae S288c | ||
| 6 | F (M) | Intron_BPS | polymer | 29 | 9161.4 | 1 | Saccharomyces cerevisiae S288c | ||
| 7 | G (B) | 5'-Exon | polymer | 13 | 4112.5 | 1 | Saccharomyces cerevisiae S288c | ||
| 8 | H (N) | 5'-Splicing Site | polymer | 15 | 4694.7 | 1 | Saccharomyces cerevisiae S288c | ||
| 9 | I (J) | Pre-mRNA-splicing factor CWC21 | polymer | 135 | 15793.6 | 1 | UniProt (Q03375) Pfam (PF08312) | Saccharomyces cerevisiae S288C | Complexed with CEF1 protein 21 |
| 10 | J (O) | Pre-mRNA-splicing factor PRP46 | polymer | 451 | 50771.3 | 1 | UniProt (Q12417) Pfam (PF00400) | Saccharomyces cerevisiae S288C | Pre-mRNA-processing protein 46 |
| 11 | K (P) | Pre-mRNA-processing protein 45 | polymer | 379 | 42548.7 | 1 | UniProt (P28004) Pfam (PF02731) | Saccharomyces cerevisiae S288C | |
| 12 | L (Q) | Pre-mRNA-splicing factor SLT11 | polymer | 364 | 40988.6 | 1 | UniProt (P38241) Pfam (PF21369) | Saccharomyces cerevisiae S288C | Synthetic lethality with U2 protein 11 |
| 13 | M (R) | Pre-mRNA-splicing factor CWC2 | polymer | 339 | 38486.6 | 1 | UniProt (Q12046) Pfam (PF16131) Pfam (PF00076) | Saccharomyces cerevisiae S288C | Complexed with CEF1 protein 2 |
| 14 | N (S) | Pre-mRNA-splicing factor CWC15 | polymer | 175 | 19975.2 | 1 | UniProt (Q03772) Pfam (PF04889) | Saccharomyces cerevisiae S288C | Complexed with CEF1 protein 15 |
| 15 | O (T) | Pre-mRNA-splicing factor BUD31 | polymer | 157 | 18484.5 | 1 | UniProt (P25337) Pfam (PF01125) | Saccharomyces cerevisiae S288C | Bud site selection protein 31,Complexed with CEF1 protein 14 |
| 16 | P (Z) | Pre-mRNA-splicing factor CWC22 | polymer | 577 | 67386.1 | 1 | UniProt (P53333) Pfam (PF02847) | Saccharomyces cerevisiae S288C | Complexed with CEF1 protein 22 |
| 17 | Q (c) | Pre-mRNA-splicing factor CEF1 | polymer | 587 | 61057.6 | 1 | UniProt (Q03654) Pfam (PF00249) Pfam (PF11831) | Saccharomyces cerevisiae S288C | |
| 18 | R (d) | Pre-mRNA-splicing factor CLF1 | polymer | 687 | 68044.6 | 1 | UniProt (Q12309) Pfam (PF23233) | Saccharomyces cerevisiae S288C | Crooked neck-like factor 1 |
| 19 | S (F) | Protein CWC16 | polymer | 278 | 32371.1 | 1 | UniProt (P28320) Pfam (PF04502) | Saccharomyces cerevisiae S288C | |
| 20 | T (G) | Pre-mRNA-splicing factor CWC25 | polymer | 179 | 20412.5 | 1 | UniProt (P53854) Pfam (PF10197) Pfam (PF12542) | Saccharomyces cerevisiae S288C | Complexed with CEF1 protein 25 |
| 21 | U (H) | Pre-mRNA-splicing factor ISY1 | polymer | 235 | 28073.8 | 1 | UniProt (P21374) Pfam (PF06246) | Saccharomyces cerevisiae S288C | Interactor of SYF1 |
| 22 | V (I) | Pre-mRNA-splicing factor SYF2 | polymer | 215 | 24850.7 | 1 | UniProt (P53277) Pfam (PF08231) | Saccharomyces cerevisiae S288C | Synthetic lethal with CDC40 protein 2 |
| 23 | W (v) | Pre-mRNA-splicing factor SYF1 | polymer | 859 | 78125.6 | 1 | UniProt (Q04048) Pfam (PF23231) | Saccharomyces cerevisiae S288c | Synthetic lethal with CDC40 protein 1 |
| 24 | X (n) | Pre-mRNA-processing factor 17 | polymer | 455 | 52128.8 | 1 | UniProt (P40968) Pfam (PF00400) | Saccharomyces cerevisiae S288C | |
| 25 | AA, BA, Y, Z (o, p, q, r) | Pre-mRNA-processing factor 19 | polymer | 503 | 56629.8 | 4 | UniProt (P32523) Pfam (PF08606) | Saccharomyces cerevisiae S288C | |
| 26 | CA (t) | Pre-mRNA-splicing factor SNT309 | polymer | 175 | 20741.5 | 1 | UniProt (Q06091) | Saccharomyces cerevisiae S288C | Synergistic to PRP19 mutation protein 309 |
| 27 | DA, KA (k, s) | Small nuclear ribonucleoprotein-associated protein B | polymer | 196 | 22427.0 | 2 | UniProt (P40018) Pfam (PF01423) | Saccharomyces cerevisiae S288C | snRNP-B,Sm protein B,SmB |
| 28 | EA, LA (i, u) | Small nuclear ribonucleoprotein E | polymer | 94 | 10385.1 | 2 | UniProt (Q12330) Pfam (PF01423) | Saccharomyces cerevisiae S288C | snRNP-E,Sm protein E,SmE |
| 29 | FA, MA (h, w) | Small nuclear ribonucleoprotein F | polymer | 86 | 9669.9 | 2 | UniProt (P54999) Pfam (PF01423) | Saccharomyces cerevisiae S288C | snRNP-F,Sm protein F,SmF |
| 30 | GA, NA (j, x) | Small nuclear ribonucleoprotein G | polymer | 77 | 8490.8 | 2 | UniProt (P40204) Pfam (PF01423) | Saccharomyces cerevisiae S288C | snRNP-G,Sm protein G,SmG |
| 31 | HA, OA (l, y) | Small nuclear ribonucleoprotein Sm D3 | polymer | 101 | 11240.1 | 2 | UniProt (P43321) Pfam (PF01423) | Saccharomyces cerevisiae S288C | Sm-D3,snRNP core protein D3 |
| 32 | IA, PA (m, z) | Small nuclear ribonucleoprotein Sm D1 | polymer | 146 | 16296.8 | 2 | UniProt (Q02260) Pfam (PF01423) | Saccharomyces cerevisiae S288C | Sm-D1,snRNP core protein D1 |
| 33 | JA, QA (g, e) | Small nuclear ribonucleoprotein Sm D2 | polymer | 110 | 12876.1 | 2 | UniProt (Q06217) Pfam (PF01423) | Saccharomyces cerevisiae S288C | Sm-D2,snRNP core protein D2 |
| 34 | RA (a) | U2 small nuclear ribonucleoprotein B'' | polymer | 111 | 12850.9 | 1 | UniProt (P40567) Pfam (PF13893) | Saccharomyces cerevisiae S288C | U2 snRNP B'' |
| 35 | SA (b) | U2 small nuclear ribonucleoprotein A' | polymer | 238 | 27232.3 | 1 | UniProt (Q08963) Pfam (PF14580) | Saccharomyces cerevisiae S288C | U2 snRNP A',Looks exceptionally like U2A protein 1 |
| 36 | TA (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) | |||
| 37 | UA, VA, WA, XA, YA... (C, E) | MAGNESIUM ION | non-polymer | 24.3 | 6 | Chemie (MG) PubChem (888) | |||
| 38 | AB, BB, CB, DB, EB... (Q, R, T, F) | ZINC ION | non-polymer | 65.4 | 7 | Chemie (ZN) |
Sequence modifications
c: 1 - 253 (UniProt: Q03654)
c: 253 - 469 (PDB: 5GMK)
c: 482 - 587 (UniProt: Q03654)
d: 1 - 275 (UniProt: Q12309)
d: 295 - 744 (PDB: 5GMK)
v: -39 - 561 (PDB: 5GMK)
v: 569 - 734 (UniProt: Q04048)
v: 740 - 867 (PDB: 5GMK)
c: 253 - 469 (PDB: 5GMK)
c: 482 - 587 (UniProt: Q03654)
d: 1 - 275 (UniProt: Q12309)
d: 295 - 744 (PDB: 5GMK)
v: -39 - 561 (PDB: 5GMK)
v: 569 - 734 (UniProt: Q04048)
v: 740 - 867 (PDB: 5GMK)
Sequence viewer
Contents of the asymmetric unit
| Polymers | Number of chains | 45 |
| Total formula weight | 2022418.6 | |
| Non-Polymers* | Number of molecules | 14 |
| Total formula weight | 1126.9 | |
| All* | Total formula weight | 2023545.5 |
