Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8cah
Q-score: 0.43
Ikeuchi K, Ivic N, Buschauer R, Cheng J, Frohlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R
Nat Commun (2023) 14 pp. 2730-2730 [ Pubmed: 37169754 DOI: doi:10.1038/s41467-023-38161-w ]
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui1 isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Rna recognition motif (unknown) (6 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s31 (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Iron/sulfur cluster (351 Da, Ligand)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Yeast native 43s pre-initiation complex with deubiquitinating enzyme otu2 bound to ubiquitinated es7 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit j (29 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l40-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit g (30 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s26-a (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 4c (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Rli1 isoform 1 (68 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8cas
Q-score: 0.366
Ikeuchi K, Ivic N, Buschauer R, Cheng J, Frohlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R
Nat Commun (2023) 14 pp. 2730-2730 [ Pubmed: 37169754 DOI: doi:10.1038/s41467-023-38161-w ]
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- Trna (24 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s31 (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Protein-synthesizing gtpase (57 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Mrna (2 kDa, RNA from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Methionine (149 Da, Ligand)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui3 isoform 1 (31 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l40-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui2 isoform 1 (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit g (30 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s26-a (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 4c (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Tif5 isoform 1 (45 kDa, Protein from Saccharomyces cerevisiae W303)
- Rli1 isoform 1 (68 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- Yeast native 48s initiation complex (partial) with deubiquitinating enzyme otu2 bound to ubiquitinated es7 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
Yeast cytoplasmic pre-40S ribosome biogenesis complex with deubiquitinating enzyme Otu2
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8cbj
Q-score: 0.263
Ikeuchi K, Ivic N, Buschauer R, Cheng J, Frohlich T, Matsuo Y, Berninghausen O, Inada T, Becker T, Beckmann R
Nat Commun (2023) 14 pp. 2730-2730 [ Pubmed: 37169754 DOI: doi:10.1038/s41467-023-38161-w ]
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- Non-specific serine/threonine protein kinase (49 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Saccharomyces cerevisiae W303)
- Yeast cytoplasmic pre-40s ribosome biogenesis complex with deubiquitinating enzyme otu2 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- Rrna adenine n(6)-methyltransferase (36 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Ltv1 isoform 1 (53 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s-pre-rrna d-site endonuclease nob1 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s pre-ribosomal rna (647 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- Enp1 isoform 1 (55 kDa, Protein from Saccharomyces cerevisiae W303)
- Tsr1 isoform 1 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)