Cryo-EM structure of a nucleolar pre-60S ribosome (Rpf1-TAP)
Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 5z3g
Q-score: 0.422
Zhou D, Zhu X, Zheng S, Tan D, Dong MQ, Ye K
Protein Cell (2019) 10 pp. 120-130 [ DOI: doi:10.1007/s13238-018-0526-7 Pubmed: 29557065 ]
- 60s ribosomal protein l13-a (22 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l33-a (12 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l20-a (20 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l14-a (15 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l18-a (20 kDa, Protein from Saccharomyces cerevisiae S288c)
- 25s rrna (1 MDa, RNA from Saccharomyces cerevisiae)
- Ribosome biogenesis protein 15 (25 kDa, Protein from Saccharomyces cerevisiae S288c)
- Rpf1-tap pre-60s (Complex from Saccharomyces cerevisiae)
- 60s ribosomal protein l4-a (39 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l32 (14 kDa, Protein from Saccharomyces cerevisiae S288c)
- Nucleolar protein 7 (69 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l9-a (21 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l17-a (20 kDa, Protein from Saccharomyces cerevisiae S288c)
- Protein mak16 (35 kDa, Protein from Saccharomyces cerevisiae S288c)
- Rrna-processing protein ebp2 (49 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l26-a (14 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l35-a (13 kDa, Protein from Saccharomyces cerevisiae S288c)
- Its2 rna (74 kDa, RNA from Saccharomyces cerevisiae)
- 60s ribosomal protein l7-a (27 kDa, Protein from Saccharomyces cerevisiae S288c)
- 5.8s rrna (50 kDa, RNA from Saccharomyces cerevisiae)
- Proteasome-interacting protein cic1 (42 kDa, Protein from Saccharomyces cerevisiae S288c)
- Atp-dependent rna helicase has1 (56 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l15-a (24 kDa, Protein from Saccharomyces cerevisiae S288c)
- Ribosome production factor 1 (35 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l36-a (11 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l3 (43 kDa, Protein from Saccharomyces cerevisiae S288c)
- Unassigned (13 kDa, Protein from Saccharomyces cerevisiae)
- Ribosome biogenesis protein brx1 (33 kDa, Protein from Saccharomyces cerevisiae S288c)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l6-a (20 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l8-a (28 kDa, Protein from Saccharomyces cerevisiae S288c)
- Ribosome biogenesis protein nsa1 (51 kDa, Protein from Saccharomyces cerevisiae S288c)
- Ribosomal rna-processing protein 1 (33 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l37-a (9 kDa, Protein from Saccharomyces cerevisiae S288c)
- Ribosome biogenesis protein rlp7 (36 kDa, Protein from Saccharomyces cerevisiae S288c)
- 60s ribosomal protein l16-a (22 kDa, Protein from Saccharomyces cerevisiae S288c)
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 [ DOI: doi:10.1126/science.aar3729 Pubmed: 29146871 ]
- U5 snrna (57 kDa, RNA from Baker's yeast)
- Pre-mrna-splicing factor cwc15 (19 kDa, Protein from Baker's yeast)
- Inositol hexakisphosphate (660 Da, Ligand)
- Pre-mrna-splicing factor cef1 (67 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein b'' (12 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d1 (16 kDa, Protein from Baker's yeast)
- Zinc ion (65 Da, Ligand)
- Pre-mrna-splicing factor cwc16 (32 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc22 (67 kDa, Protein from Baker's yeast)
- 3' exon (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Pre-mrna-processing factor prp17 (52 kDa, Protein from Baker's yeast)
- P complex spliceosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- U2 snrna (376 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor clf1 (82 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor atp-dependent rna helicase prp22 (130 kDa, Protein from Baker's yeast)
- U6 snrna (35 kDa, RNA from Baker's yeast)
- Small nuclear ribonucleoprotein sm d3 (11 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snt309 (20 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp46 (50 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor prp8 (279 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc2 (38 kDa, Protein from Baker's yeast)
- Intron lariat: ubc4 rna (30 kDa, RNA from Saccharomyces cerevisiae S288c)
- Small nuclear ribonucleoprotein e (10 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor cwc21 (15 kDa, Protein from Baker's yeast)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Pre-mrna-splicing factor bud31 (18 kDa, Protein from Baker's yeast)
- Pre-mrna-processing protein 45 (42 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein-associated protein b (22 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor snu114 (114 kDa, Protein from Baker's yeast)
- U2 small nuclear ribonucleoprotein a' (27 kDa, Protein from Baker's yeast)
- Magnesium ion (24 Da, Ligand)
- Pre-mrna-splicing factor slu7 (44 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf2 (24 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein g (8 kDa, Protein from Baker's yeast)
- Ligated exons: ubc4 mrna (12 kDa, RNA from Saccharomyces cerevisiae S288c)
- Pre-mrna-splicing factor prp18 (28 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein sm d2 (12 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor syf1 (100 kDa, Protein from Baker's yeast)
- Small nuclear ribonucleoprotein f (9 kDa, Protein from Baker's yeast)
- Pre-mrna-processing factor prp19 (56 kDa, Protein from Baker's yeast)
- Unassigned structure (8 kDa, Protein from Baker's yeast)
- Pre-mrna-splicing factor slt11 (40 kDa, Protein from Baker's yeast)
- P complex spliceosome with 3' exon docked (2 MDa, Complex)