Do data resources managed by EMBL-EBI and our collaborators make a difference to your work? Please take 10 minutes to fill in our annual user survey, and help us make the case for why sustaining open data resources is critical for life sciences research. We appreciate your responses prior to closing of the survey on Monday 17th June.
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 8bgu
Q-score: 0.321
Castillo Duque de Estrada NM, Thoms M, Flemming D, Hammaren HM, Buschauer R, Ameismeier M, Bassler J, Beck M, Beckmann R, Hurt E
Nat Struct Mol Biol (2023) 30 pp. 1119-1131 [ DOI: doi:10.1038/s41594-023-01006-7 Pubmed: 37291423 ]
- 5s rrna (38 kDa, RNA from Saccharomyces cerevisiae)
- Human mdm2-5s rnp (Complex from Homo sapiens)
- 60s ribosomal protein l11 (20 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase mdm2 (55 kDa, Protein from Homo sapiens)
- 60s ribosomal protein l5 (34 kDa, Protein from Homo sapiens)
hexameric ct-sc 5S RNP monomer
Castillo Duque de Estrada NM, Thoms M, Flemming D, Hammaren HM, Buschauer R, Ameismeier M, Bassler J, Beck M, Beckmann R, Hurt E
Nat Struct Mol Biol (2023) 30 pp. 1119-1131 [ DOI: doi:10.1038/s41594-023-01006-7 Pubmed: 37291423 ]
Castillo Duque de Estrada NM, Thoms M, Flemming D, Hammaren HM, Buschauer R, Ameismeier M, Bassler J, Beck M, Beckmann R, Hurt E
Nat Struct Mol Biol (2023) 30 pp. 1119-1131 [ DOI: doi:10.1038/s41594-023-01006-7 Pubmed: 37291423 ]
Castillo Duque de Estrada NM, Thoms M, Flemming D, Hammaren HM, Buschauer R, Ameismeier M, Bassler J, Beck M, Beckmann R, Hurt E
Nat Struct Mol Biol (2023) 30 pp. 1119-1131 [ DOI: doi:10.1038/s41594-023-01006-7 Pubmed: 37291423 ]
Cryo-EM structure of in vitro reconstituted Otu2-bound Ub-40S complex - body 1
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8c83
Q-score: 0.441
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 s6-a (27 kDa, Protein from baker's yeast)
- 40s ribosomal protein s21-a (9 kDa, Protein from baker's yeast)
- 40s ribosomal protein s11-a (17 kDa, Protein from baker's yeast)
- Ubiquitin (8 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s8-b (22 kDa, Protein from baker's yeast)
- 18s ribosomal rna (579 kDa, RNA from baker's yeast)
- Otu domain-containing protein 2; ubiquitin (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s9-a (22 kDa, Protein from baker's yeast)
- 40s ribosomal protein s22-a (14 kDa, Protein from baker's yeast)
- 40s ribosomal protein s0-a (28 kDa, Protein from baker's yeast)
- 40s ribosomal protein s13 (17 kDa, Protein from baker's yeast)
- 40s ribosomal protein s4-a (29 kDa, Protein from baker's yeast)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae)
- In vitro reconstituted yeast 40s ribosome complex with deubiquitinating enzyme otu2 bound to ubiquitinated es7 - body 1 (Complex)
- 40s ribosomal protein s7-a (21 kDa, Protein from baker's yeast)
- 40s ribosomal protein s27-a (8 kDa, Protein from baker's yeast)
- 40s ribosomal protein s23-a (16 kDa, Protein from baker's yeast)
- Yeast 40s ribosome complex (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s2 (27 kDa, Protein from baker's yeast)
- 40s ribosomal protein s24-a (15 kDa, Protein from baker's yeast)
- 40s ribosomal protein s30-a (7 kDa, Protein from baker's yeast)
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 ]
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 ]
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s31 (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 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 s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 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)
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Eukaryotic translation initiation factor 3 subunit j (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui1 isoform 1 (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae W303)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l40-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Iron/sulfur cluster (351 Da, Ligand)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 4c (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Rli1 isoform 1 (68 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Rna recognition motif (unknown) (6 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 ]
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s31 (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui3 isoform 1 (31 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s26-a (13 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit g (30 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit a (110 kDa, Protein from Saccharomyces cerevisiae W303)
- Mrna (2 kDa, RNA from Saccharomyces cerevisiae)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
- Trna (24 kDa, RNA from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit b (88 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit c (93 kDa, Protein from Saccharomyces cerevisiae W303)
- Yeast native 48s initiation complex (partial) with deubiquitinating enzyme otu2 bound to ubiquitinated es7 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l41-a (3 kDa, Protein from Saccharomyces cerevisiae W303)
- Phosphomethylphosphonic acid guanylate ester (521 Da, Ligand)
- 18s ribosomal rna (579 kDa, RNA from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 3 subunit i (38 kDa, Protein from Saccharomyces cerevisiae W303)
- 60s ribosomal protein l40-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- Iron/sulfur cluster (351 Da, Ligand)
- 40s ribosomal protein s10-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Eukaryotic translation initiation factor 4c (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s30-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps29a isoform 1 (6 kDa, Protein from Saccharomyces cerevisiae W303)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- Sui2 isoform 1 (34 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Rli1 isoform 1 (68 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- Protein-synthesizing gtpase (57 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Tif5 isoform 1 (45 kDa, Protein from Saccharomyces cerevisiae W303)
- Methionine (149 Da, Ligand)
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 s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s-pre-rrna d-site endonuclease nob1 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- Non-specific serine/threonine protein kinase (49 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s23-a (16 kDa, Protein from Saccharomyces cerevisiae W303)
- Yeast cytoplasmic pre-40s ribosome biogenesis complex with deubiquitinating enzyme otu2 (Complex from Saccharomyces cerevisiae)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s2 (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s0-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from baker's yeast)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s pre-ribosomal rna (647 kDa, RNA from Saccharomyces cerevisiae)
- Rrna adenine n(6)-methyltransferase (36 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s30-a (7 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 s17-a (15 kDa, Protein from baker's yeast)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- Enp1 isoform 1 (55 kDa, Protein from Saccharomyces cerevisiae W303)
- Ltv1 isoform 1 (53 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- Tsr1 isoform 1 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
Local refinement map of Otu2 N-terminal domain bound to yeast 40S ribosome
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 ]