Structure of a B-state intermediate committed to discard (Bd-I state)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9esh
Q-score: 0.324
Soni K, Horvath A, Dybkov O, Schwan M, Trakansuebkul S, Flemming D, Wild K, Urlaub H, Fischer T, Sinning I
Nat Struct Mol Biol (2025) [ Pubmed: 39833470 DOI: doi:10.1038/s41594-024-01480-7 ]
- Pre-mrna-splicing factor cwf11 (148 kDa, Protein from Schizosaccharomyces pombe)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Schizosaccharomyces pombe)
- U2snrna (59 kDa, RNA from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf5 (39 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf21 (34 kDa, Protein from Schizosaccharomyces pombe)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cwf2 (44 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf7 (21 kDa, Protein from Schizosaccharomyces pombe)
- Unk1 (1 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor spp42 (274 kDa, Protein from Schizosaccharomyces pombe)
- Peptidyl-prolyl cis-trans isomerase ppi1 (16 kDa, Protein from Schizosaccharomyces pombe)
- U5snrna (38 kDa, RNA from Schizosaccharomyces pombe)
- Bd-i complex (Complex from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf14 (17 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf10 (111 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf3 (92 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf17 (37 kDa, Protein from Schizosaccharomyces pombe)
- Uncharacterized protein c20h4.06c (60 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing factor 19 (54 kDa, Protein from Schizosaccharomyces pombe)
- U6snrna (31 kDa, RNA from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf15 (30 kDa, Protein from Schizosaccharomyces pombe)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwf4 (80 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf22 (102 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor prp5 (52 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cdc5 (86 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein e (9 kDa, Protein from Schizosaccharomyces pombe)
- G-patch domain-containing protein c1486.03 (91 kDa, Protein from Schizosaccharomyces pombe)
- Unk2 (29 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna (9 kDa, RNA from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein f (8 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing factor 17 (63 kDa, Protein from Schizosaccharomyces pombe)
- Inositol hexakisphosphate (660 Da, Ligand)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Schizosaccharomyces pombe)
- Putative pre-mrna-splicing factor atp-dependent rna helicase c20h4.09 (73 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing protein 45 (62 kDa, Protein from Schizosaccharomyces pombe)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein-associated protein b (15 kDa, Protein from Schizosaccharomyces pombe)
Structure of a B-state intermediate committed to discard (Bd-II state)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 9esi
Q-score: 0.364
Soni K, Horvath A, Dybkov O, Schwan M, Trakansuebkul S, Flemming D, Wild K, Urlaub H, Fischer T, Sinning I
Nat Struct Mol Biol (2025) [ Pubmed: 39833470 DOI: doi:10.1038/s41594-024-01480-7 ]
- Pre-mrna-splicing factor cwf11 (148 kDa, Protein from Schizosaccharomyces pombe)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Schizosaccharomyces pombe)
- U2snrna (59 kDa, RNA from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf5 (39 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf21 (34 kDa, Protein from Schizosaccharomyces pombe)
- Magnesium ion (24 Da, Ligand)
- Protein saf4 (34 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf2 (44 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf7 (21 kDa, Protein from Schizosaccharomyces pombe)
- Stress response protein bis1 (43 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor spp42 (274 kDa, Protein from Schizosaccharomyces pombe)
- Unk1 (29 kDa, Protein from Schizosaccharomyces pombe)
- Peptidyl-prolyl cis-trans isomerase ppi1 (16 kDa, Protein from Schizosaccharomyces pombe)
- U5snrna (38 kDa, RNA from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf14 (17 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf10 (111 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf3 (92 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf17 (37 kDa, Protein from Schizosaccharomyces pombe)
- Uncharacterized protein c20h4.06c (60 kDa, Protein from Schizosaccharomyces pombe)
- Uncharacterized protein c17a2.08c (41 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing factor 19 (54 kDa, Protein from Schizosaccharomyces pombe)
- U6snrna (31 kDa, RNA from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf15 (30 kDa, Protein from Schizosaccharomyces pombe)
- Unk3 (1 kDa, Protein from Schizosaccharomyces pombe)
- Zinc ion (65 Da, Ligand)
- Bd-ii complex (Complex from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf4 (80 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cwf22 (102 kDa, Protein from Schizosaccharomyces pombe)
- Unk2 (4 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor prp5 (52 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-splicing factor cdc5 (86 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein e (9 kDa, Protein from Schizosaccharomyces pombe)
- G-patch domain-containing protein c1486.03 (91 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein f (8 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing factor 17 (63 kDa, Protein from Schizosaccharomyces pombe)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna (9 kDa, RNA from Schizosaccharomyces pombe)
- Inositol hexakisphosphate (660 Da, Ligand)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Schizosaccharomyces pombe)
- Putative pre-mrna-splicing factor atp-dependent rna helicase c20h4.09 (73 kDa, Protein from Schizosaccharomyces pombe)
- Pre-mrna-processing protein 45 (62 kDa, Protein from Schizosaccharomyces pombe)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein-associated protein b (15 kDa, Protein from Schizosaccharomyces pombe)
Saccharomyces cerevisiae spliceosomal E complex (UBC4)
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6n7p
Q-score: 0.352
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R
Nature (2019) 573 pp. 375-380 [ DOI: doi:10.1038/s41586-019-1523-6 Pubmed: 31485080 ]
- U1 small nuclear ribonucleoprotein component snu71,u1 small nuclear ribonucleoprotein component snu71,snu71 (10 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein c (27 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear cap-binding protein subunit 2 (23 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 g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubc4 pre-mrna (81 kDa, RNA from Saccharomyces cerevisiae S288C)
- U1 small nuclear ribonucleoprotein component prp42 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing protein prp40 (69 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 56 kda u1 small nuclear ribonucleoprotein component (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein nam8 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein a (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein luc7 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Nuclear cap-binding protein complex subunit 1 (100 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing factor 39 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Saccharomyces cerevisiae spliceosomal e complex (ebc4) (Complex from Saccharomyces cerevisiae)
- U1 small nuclear ribonucleoprotein 70 kda homolog (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 snrna (182 kDa, RNA from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Saccharomyces cerevisiae spliceosomal E complex (ACT1)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6n7r
Q-score: 0.427
Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R
Nature (2019) 573 pp. 375-380 [ DOI: doi:10.1038/s41586-019-1523-6 Pubmed: 31485080 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein c (27 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 g (8 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein component prp42 (65 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 56 kda u1 small nuclear ribonucleoprotein component (56 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein nam8 (57 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein a (40 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Protein luc7 (30 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Act1 pre-mrna (70 kDa, RNA from Saccharomyces cerevisiae S288C)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- Saccharomyces cerevisiae spliceosomal e complex (act1) (Complex from Saccharomyces cerevisiae)
- U1 snrna (182 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein component snu71,u1 small nuclear ribonucleoprotein component snu71,snu71 (9 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-processing factor 39 (74 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U1 small nuclear ribonucleoprotein 70 kda homolog (34 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Structure of a human fully-assembled precatalytic spliceosome (pre-B complex).
Resolution: 3.28 Å
EM Method: Single-particle
Fitted PDBs: 6qx9
Q-score: 0.207
Charenton C, Wilkinson ME, Nagai K
Science (2019) 364 pp. 362-367 [ DOI: doi:10.1126/science.aax3289 Pubmed: 30975767 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- U4/u6 small nuclear ribonucleoprotein prp31 (55 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 3 (135 kDa, Protein from Homo sapiens)
- U4/u6 small nuclear ribonucleoprotein prp4 (58 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 4 (44 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (271 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Nhp2-like protein 1 (14 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm3 (11 kDa, Protein from Homo sapiens)
- Thioredoxin-like protein 4a (16 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm6 (9 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (13 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d3 (13 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm7 (11 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm4 (15 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 6 (97 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm5 (9 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 1 (146 kDa, Protein from Homo sapiens)
- U4/u6 small nuclear ribonucleoprotein prp3 (77 kDa, Protein from Homo sapiens)
- U5 snrna (37 kDa, RNA from Homo sapiens)
- Adml pre-mrna (15 kDa, RNA from Human adenovirus 2)
- U1 snrna (52 kDa, RNA from Homo sapiens)
- Splicing factor 3a subunit 1,splicing factor 3a subunit 1,splicing factor 3a subunit 1 (71 kDa, Protein from Homo sapiens)
- Splicing factor 3b subunit 5 (10 kDa, Protein from Homo sapiens)
- U4/u6.u5 tri-snrnp-associated protein 2 (64 kDa, Protein from Homo sapiens)
- U4 snrna (46 kDa, RNA from Homo sapiens)
- Phd finger-like domain-containing protein 5a (11 kDa, Protein from Homo sapiens)
- Rna-binding protein 42 (50 kDa, Protein from Homo sapiens)
- U6 snrna-associated sm-like protein lsm8 (10 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 40 kda protein (39 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Fully-assembled precatalytic spliceosome (pre-b complex). (3 MDa, Complex)
- Splicing factor 3b subunit 2 (100 kDa, Protein from Homo sapiens)
- Probable atp-dependent rna helicase ddx23 (Complex from Homo sapiens)
- Probable atp-dependent rna helicase ddx23 (95 kDa, Protein from Homo sapiens)
- U1 small nuclear ribonucleoprotein a (31 kDa, Protein from Homo sapiens)
- U4/u6.u5 tri-snrnp-associated protein 1 (90 kDa, Protein from Homo sapiens)
- Splicing factor 3a subunit 3 (58 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 200 kda helicase (244 kDa, Protein from Homo sapiens)
- Serine/threonine-protein kinase prp4 homolog (117 kDa, Protein from Homo sapiens)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Adml pre-mrna (Complex from Human adenovirus 2)
- U6 snrna-associated sm-like protein lsm2 (10 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- 116 kda u5 small nuclear ribonucleoprotein component (95 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- U1 small nuclear ribonucleoprotein 70 kda (51 kDa, Protein from Homo sapiens)
- Fully-assembled precatalytic spliceosome (pre-b complex). (Complex from Homo sapiens)
- Splicing factor 3a subunit 2 (24 kDa, Protein from Homo sapiens)
- U4/u6.u5 small nuclear ribonucleoprotein 27 kda protein (18 kDa, Protein from Homo sapiens)
- U1 small nuclear ribonucleoprotein c (17 kDa, Protein from Homo sapiens)
Human post-catalytic spliceosome (P complex) stalled with DHX8 K594A mutant, overall map
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 6qdv
Q-score: 0.278
Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K
Science (2019) 363 pp. 710-714 [ DOI: doi:10.1126/science.aaw5569 Pubmed: 30705154 ]
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Human post-catalytic p complex spliceosome (3 MDa, Complex)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Eukaryotic initiation factor 4a-iii, n-terminally processed (44 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- Small nuclear ribonucleoprotein f (8 kDa, Protein from Homo sapiens)
- Cactin (15 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (33 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Ligated exons: minx mrna (4 kDa, RNA from Human adenovirus 2)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (9 kDa, Protein from Homo sapiens)
- Crooked neck-like protein 1 (100 kDa, Protein from Homo sapiens)
- Minx introns and exons (Complex from Human adenovirus 2)
- Magnesium ion (24 Da, Ligand)
- Small nuclear ribonucleoprotein-associated proteins b and b' (9 kDa, Protein from Homo sapiens)
- Prkr-interacting protein 1 (14 kDa, Protein from Homo sapiens)
- Replication stress response regulator sde2 (4 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d1 (9 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Homo sapiens)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Protein fam32a (7 kDa, Protein from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (101 kDa, Protein from Homo sapiens)
- Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Atp-dependent rna helicase dhx8 (Complex from Homo sapiens)
- Nf-kappa-b-activating protein (3 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (18 kDa, Protein from Homo sapiens)
- Human post-catalytic p complex spliceosome (Complex from Homo sapiens)
- Snw domain-containing protein 1 (33 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (35 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein sm d3 (9 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 200 kda helicase (197 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (10 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (2 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 1 (18 kDa, Protein from Homo sapiens)
- U5 small nuclear ribonucleoprotein 40 kda protein (34 kDa, Protein from Homo sapiens)
- Intron lariat: minx rna (27 kDa, RNA from Human adenovirus 2)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 17 (59 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Protein mago nashi homolog 2 (16 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (17 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Rna-binding protein 8a (10 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor cwc22 homolog (105 kDa, Protein from Homo sapiens)
Post-catalytic P complex spliceosome with 3' splice site docked
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 6exn
Q-score: 0.296
Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K
Science (2017) 358 pp. 1283-1288 [ Pubmed: 29146871 DOI: doi:10.1126/science.aar3729 ]
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Baker's yeast)
- Ligated exons: ubc4 mrna (12 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-processing factor prp19 (56 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor prp17 (52 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor prp8 (279 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 3' exon (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc16 (32 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- U5 snrna (57 kDa, RNA from Baker's yeast)
- Intron lariat: ubc4 rna (30 kDa, RNA from Saccharomyces cerevisiae S288c)
- U6 snrna (35 kDa, RNA from Baker's yeast)
- Unassigned structure (8 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- P complex spliceosome with 3' exon docked (2 MDa, Complex)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- P complex spliceosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor prp18 (28 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
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 ]
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Unknown (5 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1 (101 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Yeast ubc4 gene for ubiquitin-conjugating enzyme (30 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 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)
- Zinc ion (65 Da, Ligand)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae spliceosome. complex c just after prp16-mediated remodeling (Complex)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Inositol hexakisphosphate (660 Da, Ligand)
- Ubc4 gene exon (6 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Overall map of the yeast spliceosome immediately after branching
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 5lj3
Q-score: 0.328
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 ]
- U5 snrna (small nuclear rna) (57 kDa, RNA from Saccharomyces cerevisiae)
- U2 snrna (small nuclear rna) (376 kDa, RNA from Saccharomyces cerevisiae)
- Exon 1 (5' exon) of ubc4 pre-mrna (5 kDa, RNA from Saccharomyces cerevisiae)
- Cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae )
- Cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (small nuclear rna) (35 kDa, RNA from Saccharomyces cerevisiae)
- Isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae )
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae )
- Unknown (11 kDa, Protein from Saccharomyces cerevisiae)
- Clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae )
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae )
- Zinc ion (65 Da, Ligand)
- Intron of ubc4 pre-mrna (24 kDa, RNA from Saccharomyces cerevisiae)
- Spliceosome immediately after branching (2 MDa, Complex from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae )
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae )
- Prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae )
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae )
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Cwc22 (69 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae )
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae )
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae )
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae )
- Syf1 (100 kDa, Protein from Saccharomyces cerevisiae)
Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 5gam
Q-score: 0.363
Nguyen THD, Galej WP, Bai XC, Oubridge C, Scheres SHW, Newman AJ, Nagai K
Nature (2016) 530 pp. 298-302 [ Pubmed: 26829225 DOI: doi:10.1038/nature16940 ]
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Foot region of the yeast spliceosomal u4/u6.u5 tri-snrnp (350 kDa, Complex from Saccharomyces cerevisiae)
- Unknown polypeptide (1 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (57 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (85 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna, 5' end (9 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)