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 s1-a (28 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s28-a (7 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s5 (25 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s7-a (21 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s13 (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s17-a (15 kDa, Protein from Saccharomyces cerevisiae)
- 40s ribosomal protein s19-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s24-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
- Yeast cytoplasmic pre-40s ribosome biogenesis complex with deubiquitinating enzyme otu2 (Complex from Saccharomyces cerevisiae)
- Enp1 isoform 1 (55 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s9-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s4-b (29 kDa, Protein from Saccharomyces cerevisiae W303)
- Magnesium ion (24 Da, Ligand)
- 40s ribosomal protein s3 (26 kDa, Protein from Saccharomyces cerevisiae W303)
- Guanine nucleotide-binding protein subunit beta-like protein (34 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s18-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s23-a (16 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)
- Pre-rrna-processing protein pno1 (30 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s12 (15 kDa, Protein from Saccharomyces cerevisiae)
- Rps15 isoform 1 (16 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s-pre-rrna d-site endonuclease nob1 (51 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s8-a (22 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s20 (13 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s22-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- 20s pre-ribosomal rna (647 kDa, RNA from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
- Rrna adenine n(6)-methyltransferase (36 kDa, Protein from Saccharomyces cerevisiae W303)
- Otu domain-containing protein 2 (36 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s14-a (14 kDa, Protein from Saccharomyces cerevisiae W303)
- Tsr1 isoform 1 (90 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s21-a (9 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s25-a (12 kDa, Protein from Saccharomyces cerevisiae W303)
- Non-specific serine/threonine protein kinase (49 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s6-b (27 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)
- Ltv1 isoform 1 (53 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s11-a (17 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s27-a (8 kDa, Protein from Saccharomyces cerevisiae W303)
- 40s ribosomal protein s16-a (15 kDa, Protein from Saccharomyces cerevisiae W303)
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6zmt
Q-score: 0.489
Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R
Science (2020) 369 pp. 1249-1255 [ DOI: doi:10.1126/science.abc8665 Pubmed: 32680882 ]
- 40s ribosomal protein s7 (22 kDa, Protein from Homo sapiens)
- Ubiquitin-40s ribosomal protein s27a (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (30 kDa, Protein from Homo sapiens)
- Pre-40s-like ribosome complex (Complex from Homo sapiens)
- 40s ribosomal protein s15 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (15 kDa, Protein from Homo sapiens)
- Pre-rrna-processing protein tsr1 homolog (91 kDa, Protein from Homo sapiens)
- Non-structural protein 1 (19 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 40s ribosomal protein s16 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s5 (22 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- Sars-cov-2 nsp1 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s11 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s19 (16 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (35 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (28 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s28 (7 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (18 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s2 (31 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (13 kDa, Protein from Homo sapiens)
- Sars-cov-2 nsp1 bound to a pre-40s-like ribosome complex (Complex)
- 18s ribosomal rna (602 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (32 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (16 kDa, Protein from Homo sapiens)
SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex - state 2
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 6zn5
Q-score: 0.514
Thoms M, Buschauer R, Ameismeier M, Koepke L, Denk T, Hirschenberger M, Kratzat H, Hayn M, Mackens-Kiani T, Cheng J, Straub JH, Sturzel CM, Frohlich T, Berninghausen O, Becker T, Kirchhoff F, Sparrer KMJ, Beckmann R
Science (2020) 369 pp. 1249-1255 [ DOI: doi:10.1126/science.abc8665 Pubmed: 32680882 ]
- 40s ribosomal protein s2 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s23 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s16 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s27 (9 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s17 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s25 (8 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s11 (17 kDa, Protein from Homo sapiens)
- Pre-rrna-processing protein tsr1 homolog (91 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s26 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s20 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s15a (14 kDa, Protein from Homo sapiens)
- Non-structural protein 1 (19 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Human pre-40s-like ribosome complex (Complex from Homo sapiens)
- Ribosomal protein s27a (8 kDa, Protein from Homo sapiens)
- Receptor of activated protein c kinase 1 (34 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3a (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s14 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s24 (14 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s3 (24 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s8 (23 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s21 (8 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s13 (17 kDa, Protein from Homo sapiens)
- Sars-cov-2 nsp1 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- 40s ribosomal protein s5 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein sa (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 nsp1 bound to a human pre-40s-like ribosome complex (Complex)
- 40s ribosomal protein s19 (15 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s10 (11 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s12 (13 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s9 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s29 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s7 (21 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s18 (16 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s4, x isoform (29 kDa, Protein from Homo sapiens)
- 18s ribosomal rna (602 kDa, RNA from Homo sapiens)
- 40s ribosomal protein s28 (6 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s6 (26 kDa, Protein from Homo sapiens)
- 40s ribosomal protein s30 (6 kDa, Protein from Homo sapiens)