Structure of a group II intron ribonucleoprotein in the pre-ligation (pre-2F) state
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8t2r
Q-score: 0.459
Nature (2023) 624 pp. 682-688 [ Pubmed: 37993708 DOI: doi:10.1038/s41586-023-06746-6 ]
- Ammonium ion (18 Da, Ligand)
- Intron rnp complex in pre-2f (300 kDa, Complex from [Eubacterium] rectale)
- Group ii intron reverse transcriptase/maturase (49 kDa, Protein from [Eubacterium] rectale)
- Intron (208 kDa, RNA from [Eubacterium] rectale)
- 5'exon (2 kDa, RNA from [Eubacterium] rectale)
- Calcium ion (40 Da, Ligand)
Human spliceosomal PM5 C* complex
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8c6j
Q-score: 0.353
Dybkov O, Preussner M, El Ayoubi L, Feng VY, Harnisch C, Merz K, Leupold P, Yudichev P, Agafonov DE, Will CL, Girard C, Dienemann C, Urlaub H, Kastner B, Heyd F, Luehrmann R
Sci Adv (2023) 9 pp. eadf1785- [ Pubmed: 36867703 DOI: doi:10.1126/sciadv.adf1785 ]
- Peptidyl-prolyl cis-trans isomerase e (33 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein sm d2 (13 kDa, Protein from Homo sapiens)
- Protein bud31 homolog (17 kDa, Protein from Homo sapiens)
- Nitric oxide synthase-interacting protein (33 kDa, Protein from Homo sapiens)
- U5 snrna (36 kDa, RNA from Homo sapiens)
- Pre-mrna-splicing factor slu7 (68 kDa, Protein from Homo sapiens)
- Potassium ion (39 Da, Ligand)
- Splicing factor ess-2 homolog (52 kDa, Protein from Homo sapiens)
- Splicing factor c9orf78 (33 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein b'' (25 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein-associated proteins b and b' (24 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Homo sapiens)
- Cell division cycle 5-like protein (92 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-processing factor 17 (65 kDa, Protein from Homo sapiens)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Homo sapiens)
- Peptidyl-prolyl cis-trans isomerase-like 3 (18 kDa, Protein from Homo sapiens)
- Probable atp-dependent rna helicase ddx41 (69 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf1 (100 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)
- Atp-dependent rna helicase dhx8 (139 kDa, Protein from Homo sapiens)
- Pre-mrna-processing factor 19 (55 kDa, Protein from Homo sapiens)
- Human spliceosomal c* complex assembled on pm5 pre-mrna (Complex from Homo sapiens)
- 116 kda u5 small nuclear ribonucleoprotein component (109 kDa, Protein from Homo sapiens)
- Crooked neck-like protein 1 (83 kDa, Protein from Homo sapiens)
- Intron-binding protein aquarius (171 kDa, Protein from Homo sapiens)
- Pleiotropic regulator 1 (57 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor syf2 (28 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor rbm22 (46 kDa, Protein from Homo sapiens)
- Serine/arginine repetitive matrix protein 2 (300 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 (39 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Splicing regulator sde2 (49 kDa, Protein from Homo sapiens)
- Snw domain-containing protein 1 (61 kDa, Protein from Homo sapiens)
- Pre-mrna-processing-splicing factor 8 (273 kDa, Protein from Homo sapiens)
- Pm5 5' exon (78 kDa, RNA from Homo sapiens)
- Nf-kappa-b-activating protein (47 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)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- U6 snrna (34 kDa, RNA from Homo sapiens)
- Rna-binding protein 8a (19 kDa, Protein from Homo sapiens)
- Spliceosome-associated protein cwc15 homolog (26 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor isy1 homolog (33 kDa, Protein from Homo sapiens)
- Inositol hexakisphosphate (660 Da, Ligand)
- Protein fam50a (40 kDa, Protein from Homo sapiens)
- Sting er exit protein (25 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor spf27 (26 kDa, Protein from Homo sapiens)
- U2 snrna (60 kDa, RNA from Homo sapiens)
- Prkr-interacting protein 1 (21 kDa, Protein from Homo sapiens)
- U2 small nuclear ribonucleoprotein a' (28 kDa, Protein from Homo sapiens)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Eukaryotic initiation factor 4a-iii (46 kDa, Protein from Homo sapiens)
- Pre-mrna-splicing factor cwc22 homolog (57 kDa, Protein from Homo sapiens)
- Pm5 intron (74 kDa, RNA from Homo sapiens)
- Splicing factor cactin (88 kDa, Protein from Homo sapiens)
- Protein fam32a (13 kDa, Protein from Homo sapiens)
- Protein mago nashi homolog (17 kDa, Protein from Homo sapiens)
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- [ DOI: doi:10.1016/j.molcel.2021.02.021 Pubmed: 33705709 ]
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0054360.mrna.1.cds.1 (50 kDa, Protein from Saccharomyces cerevisiae)
- Potassium ion (39 Da, Ligand)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor isy1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 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)
- Cdc40 isoform 1 (52 kDa, Protein from Saccharomyces cerevisiae)
- Bud31 isoform 1 (18 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Ntc20 isoform 1 (15 kDa, Protein 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)
- 5' exon of ubc4 mrna (15 kDa, RNA from Saccharomyces cerevisiae)
- Splicing factor yju2 (33 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae)
- Bj4_g0027490.mrna.1.cds.1 (12 kDa, Protein from Saccharomyces cerevisiae)
- D-chiro inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Y55_g0042700.mrna.1.cds.1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Cwc22 isoform 1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Clf1 isoform 1 (82 kDa, Protein from Saccharomyces cerevisiae)
- Hlj1_g0053790.mrna.1.cds.1 (27 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae)
- Yeast c complex spliceosome with prp18/slu7 bound (2 MDa, Complex from Saccharomyces cerevisiae)
- Syf1 isoform 1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 18 (28 kDa, Protein from Saccharomyces cerevisiae)
- Snt309 isoform 1 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Branched intron and 3' exon of ubc4 pre-mrna (30 kDa, RNA from Saccharomyces cerevisiae)
- Unassigned structure (20 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor cwc15 (19 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 ]
- 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)
- 5'-exon of ubc4 pre-mrna (6 kDa, RNA from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain t.52_2h chromosome xii sequence (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 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)
- 3'-exon of ubc4 pre-mrna, bound by prp22 helicase (873 Da, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1,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)
- S.cerevisiae chromosome ii reading frame orf ybr230c (376 kDa, RNA from Saccharomyces cerevisiae)
- Saccharomyces cerevisiae strain wi_c_mbsp_4 chromosome vii sequence (57 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)
- Unknown protein (5 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)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 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)
- 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 atp-dependent rna helicase prp22 (130 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)
- 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)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
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 ]
- 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)
- Pre-mrna-splicing factor atp-dependent rna helicase prp16 (121 kDa, Protein from Saccharomyces cerevisiae)
- Cwc15 (19 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae)
- U6 snrna (small nuclear rna) (35 kDa, RNA from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing helicase brr2 (246 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)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Saccharomyces cerevisiae)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein 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-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae)
- U2 small nuclear ribonucleoprotein b'' (12 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-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Saccharomyces cerevisiae)
- Intron of ubc4 pre-mrna (24 kDa, RNA from Saccharomyces cerevisiae)
- Spliceosome immediately after branching (2 MDa, Complex from Saccharomyces cerevisiae)
- Unknown (16 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae)
- Cwc22 (69 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Saccharomyces cerevisiae)
Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5gmk
Q-score: 0.279
Wan R, Yan C, Bai R, Huang G, Shi Y
Science (2016) 353 pp. 895-904 [ Pubmed: 27445308 DOI: doi:10.1126/science.aag2235 ]
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Saccharomyces cerevisiae S288C)
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-processing factor 17 (52 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor syf1 (78 kDa, Protein from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor cef1 (61 kDa, Protein from Saccharomyces cerevisiae S288C)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Saccharomyces cerevisiae S288C)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-processing factor 19 (56 kDa, Protein from Saccharomyces cerevisiae S288C)
- Spliceosomal c complex (Complex from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor clf1 (68 kDa, Protein from Saccharomyces cerevisiae S288C)
- 5'-exon (4 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor 8 (279 kDa, Protein from Saccharomyces cerevisiae S288C)
- Zinc ion (65 Da, Ligand)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Saccharomyces cerevisiae S288C)
- U5 snrna (68 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor cwc25 (20 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor isy1 (28 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Saccharomyces cerevisiae S288C)
- U6 snrna (35 kDa, RNA from Saccharomyces cerevisiae S288c)
- 5'-splicing site (4 kDa, RNA from Saccharomyces cerevisiae S288c)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Saccharomyces cerevisiae S288C)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Saccharomyces cerevisiae S288C)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Saccharomyces cerevisiae S288C)
- Intron_bps (9 kDa, RNA from Saccharomyces cerevisiae S288c)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Saccharomyces cerevisiae S288C)
- Protein cwc16 (32 kDa, Protein from Saccharomyces cerevisiae S288C)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Saccharomyces cerevisiae S288C)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Saccharomyces cerevisiae S288C)
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)