Yeast post-catalytic P complex spliceosome, state I, overall map
Resolution: 2.31 Å
EM Method: Single-particle
Fitted PDBs: 9dtr
Q-score: 0.419
Senn KA, Lipinski KA, Zeps NJ, Griffin AF, Wilkinson ME, Hoskins AA
bioRxiv (2024) [ Pubmed: 38746449 DOI: doi:10.1101/2024.05.04.592262 ]
- Potassium ion (39 Da, Ligand)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Ubc4 mrna spliced exons (13 kDa, RNA from Saccharomyces cerevisiae)
- Ubc4 lariat-intron (30 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor ntc20 (15 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Protein fyv6 (20 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Yeast post-catalytic p complex spliceosome (2 MDa, Complex from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7dco
Q-score: 0.408
Bai R, Wan R, Yan C, Jia Q, Lei J, Shi Y
Science (2021) 371 [ DOI: doi:10.1126/science.abe8863 Pubmed: 33243853 ]
- Hlj1_g0053790.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Prp11 isoform 1 (29 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc26 (14 kDa, Protein from Saccharomyces cerevisiae)
- Cwc22 isoform 1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Syf1 isoform 1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Sm protein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Bud31 isoform 1 (18 kDa, Protein from Saccharomyces cerevisiae)
- Snt309 isoform 1 (20 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Cwc27 isoform 1 (35 kDa, Protein from Saccharomyces cerevisiae)
- Cdc40 isoform 1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0014900.mrna.1.cds.1 (22 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor spp2 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Prp8 isoform 1 (279 kDa, Protein from Saccharomyces cerevisiae)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Water (18 Da, Ligand)
- Hsh49 isoform 1 (24 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Rds3 complex subunit 10 (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Hlj1_g0043010.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Rse1 isoform 1 (153 kDa, Protein from Saccharomyces cerevisiae)
- Clf1 isoform 1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Sx2_g0027210.mrna.1.cds.1 (14 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Prp9 isoform 1 (63 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna leakage protein 1 (23 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Hlj1_g0054350.mrna.1.cds.1 (37 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0056610.mrna.1.cds.1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0027490.mrna.1.cds.1 (12 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Brr2 isoform 1 (246 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna (44 kDa, RNA from Saccharomyces cerevisiae)
- Snu114 isoform 1 (114 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0037700.mrna.1.cds.1 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase-like protein prp2 (99 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Calcium ion (40 Da, Ligand)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp21 (33 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Hsh155 isoform 1 (110 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (29 kDa, Protein from Saccharomyces cerevisiae)
- Smd1 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc24 (29 kDa, Protein from Saccharomyces cerevisiae)
- The activated spliceosome bact complex (Complex from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (8 kDa, Protein from Saccharomyces cerevisiae)
Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound, composite map
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7b9v
Q-score: 0.378
Wilkinson ME, Fica SM, Galej WP, Nagai K
Mol Cell (2021) 81 pp. 1439- [ Pubmed: 33705709 DOI: doi:10.1016/j.molcel.2021.02.021 ]
- Potassium ion (39 Da, Ligand)
- Hlj1_g0053790.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Ntc20 isoform 1 (15 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- Unassigned structure (20 kDa, Protein from Saccharomyces cerevisiae)
- Yeast c complex spliceosome with prp18/slu7 bound (2 MDa, Complex from Saccharomyces cerevisiae)
- Cwc22 isoform 1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Syf1 isoform 1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0054360.mrna.1.cds.1 (50 kDa, Protein from Saccharomyces cerevisiae)
- Bud31 isoform 1 (18 kDa, Protein from Saccharomyces cerevisiae)
- Cdc40 isoform 1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Snt309 isoform 1 (20 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- 5' exon of ubc4 mrna (15 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor isy1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Y55_g0042700.mrna.1.cds.1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Splicing factor yju2 (33 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Clf1 isoform 1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Branched intron and 3' exon of ubc4 pre-mrna (30 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0027490.mrna.1.cds.1 (12 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- D-chiro inositol hexakisphosphate (660 Da, Ligand)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
S. cerevisiae spliceosomal post-catalytic P complex
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6bk8
Q-score: 0.38
Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R
Science (2017) 358 pp. 1278-1283 [ DOI: doi:10.1126/science.aar3462 Pubmed: 29146870 ]
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Rna (34-mer) (10 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein fragment (18 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-processing factor prp17 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Msl1 (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp18 (28 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Spliceosomal p complex (Complex from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp8 (279 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Unknown protein fragment (1 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Lea1 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Rna (59-mer) (18 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor prp19 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Inositol hexakisphosphate (660 Da, Ligand)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of a spliceosome remodeled for exon ligation
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 5mps
Q-score: 0.356
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Potassium ion (39 Da, Ligand)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Ubc4 gene exon (6 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Unknown (5 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Structure of a spliceosome remodeled for exon ligation
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 5mq0
Q-score: 0.223
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Potassium ion (39 Da, Ligand)
- Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- 5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1,pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- 3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Unknown protein (5 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Saccharomyces cerevisiae)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
Structure of a spliceosome remodeled for exon ligation
Fica SM, Galej WP, Wilkinson ME, Oubridge C, Bai X-C, Newman AJ, Nagai K
Nature (2017) 542 pp. 377-380 [ DOI: doi:10.1038/nature21078 Pubmed: 28076345 ]
- Potassium ion (39 Da, Ligand)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- U6 snrna (35 kDa, RNA from Baker's yeast)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- 3'exon of ubc4 pre-mrna bound to prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Baker's yeast)
- 5'exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Intron of ubc4 pre-mrna (30 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Baker's yeast)
- U2 snrna (376 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Baker's yeast)
- U5 snrna (57 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Unknown protein (5 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 5gm6
Q-score: 0.377
Yan C, Wan R, Bai R, Huang G, Shi Y
Science (2016) 353 pp. 904-911 [ Pubmed: 27445306 DOI: doi:10.1126/science.aag0291 ]
- Pre-mrna leakage protein 1 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Cold sensitive u2 snrna suppressor 1 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor clf1 (68 kDa, Protein from Saccharomyces cerevisiae S288c)
- Peptidyl-prolyl isomerase cwc27 (35 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein sm d2 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
- U2 snrnp component ist3 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna (7 kDa, RNA from Saccharomyces cerevisiae S288c)
- Protein hsh49 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp11 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor rds3 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc24 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor syf1 (78 kDa, Protein from Saccharomyces cerevisiae S288c)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Rds3 complex subunit 10 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Bact spliceosomal complex (2 MDa, Complex from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor cef1 (61 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna (18 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor 8 (265 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc26 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor atp-dependent rna helicase-like protein prp2 (99 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saccharomyces cerevisiae strain cdrdr_sf_h chromosome vii sequence (68 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-splicing factor rse1 (153 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U2 snrnp component hsh155 (110 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of the yeast spliceosome immediately after branching. 3D class containing helicase module.
Resolution: 10.0 Å
EM Method: Single-particle
Fitted PDBs: 5lj5
Q-score: 0.114
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K
Nature (2016) 537 pp. 197-201 [ DOI: doi:10.1038/nature19316 Pubmed: 27459055 ]
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 kDa, Protein from Saccharomyces cerevisiae)
- Spliceosome immediately after branching (2 MDa, Complex from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- Exon 1 (5' exon) of ubc4 pre-mrna (5 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (small nuclear rna) (57 kDa, RNA from Saccharomyces cerevisiae)
- Cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (small nuclear rna) (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- U2 snrna (small nuclear rna) (376 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Unknown (16 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae)
- Cwc22 (69 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Intron of ubc4 pre-mrna (24 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)