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)
The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
Resolution: 3.89 Å
EM Method: Single-particle
Fitted PDBs: 7xd4
Q-score: 0.32
The pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Resolution: 3.02 Å
EM Method: Single-particle
Fitted PDBs: 7xd7
Q-score: 0.473
Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z
Nat Catal (2023) [ DOI: doi:10.1038/s41929-023-00934-3 ]
- Spermidine (145 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- The pre-tet-c state molecule of co-transcriptional folded wild-type tetrahymena group i intron with 30nt 3'/5'-exon (130 kDa, RNA from Tetrahymena thermophila)
- Co-transcriptional folded wild-type tetrahymena group i intron with 30nt 3'/5'-exon (Complex from Tetrahymena thermophila)
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 8hd6
Q-score: 0.319
Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z
Nat Catal (2023) [ DOI: doi:10.1038/s41929-023-00934-3 ]
- Spermidine (145 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Co-transcriptional folded g264a mutant tetrahymena group i intron with 6nt 5'/3'-exon and 2-aminopurine nucleoside (Complex from Tetrahymena thermophila)
- The relaxed pre-tet-s1 state molecule of co-transcriptional folded g264a mutant tetrahymena group i intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside (135 kDa, RNA from Tetrahymena thermophila)
Resolution: 3.52 Å
EM Method: Single-particle
Fitted PDBs: 8hd7
Q-score: 0.364
Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z
Nat Catal (2023) [ DOI: doi:10.1038/s41929-023-00934-3 ]
- Spermidine (145 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- The intermediate pre-tet-s1 state molecule of co-transcriptional folded g264a mutant tetrahymena group i intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside (135 kDa, RNA from Tetrahymena thermophila)
- Co-transcriptional folded g264a mutated tetrahymena group i intron with 6-nt 3'/5'-exon and 2-aminopurine nucleoside (Complex from Tetrahymena thermophila)
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)