Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknot
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7o81
Q-score: 0.447
Bhatt PR, Scaiola A, Loughran G, Leibundgut M, Kratzel A, Meurs R, Dreos R, O'Connor KM, McMillan A, Bode JW, Thiel V, Gatfield D, Atkins JF, Ban N
Science (2021) 372 pp. 1306-1313 [ DOI: doi:10.1126/science.abf3546 Pubmed: 34029205 ]
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- El24 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome stalled by the sars-cov-2 pseudoknot (Complex)
- El38 (8 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el22 (14 kDa, Protein from Oryctolagus cuniculus)
- Ul29 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- P-site trna(pro) (24 kDa, RNA from Bos taurus)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- Mrna containing sars-cov-2 sequence (69 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein el28 (15 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es21 (9 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- 60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
- Ul23 (17 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Bos taurus)
- A-site met-trna(met) (24 kDa, RNA from Bos taurus)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el13 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (Complex from Severe acute respiratory syndrome coronavirus 2)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul2 (28 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (121 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el8 (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Unknown atom or ion (Ligand)
- Ribosomal protein us5 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein es26 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- Ribosomal protein es4 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es19 (16 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 pseudoknot (Complex from Severe acute respiratory syndrome coronavirus 2)
- Edf1 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Oryctolagus cuniculus)
- Ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
Cryo-EM structure of the highly atypical cytoplasmic ribosome of Euglena gracilis
Resolution: 3.15 Å
EM Method: Single-particle
Fitted PDBs: 6zj3
Q-score: 0.548
Matzov D, Taoka M, Nobe Y, Yamauchi Y, Halfon Y, Asis N, Zimermann E, Rozenberg H, Bashan A, Bhushan S, Isobe T, Gray MW, Yonath A, Shalev-Benami M
Nucleic Acids Res (2020) 48 pp. 11750-11761 [ DOI: doi:10.1093/nar/gkaa893 Pubmed: 33091122 ]
- Ribosomal protein es31 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul22 (18 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 10 (20 kDa, RNA from Euglena gracilis)
- Ribosomal protein el39 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein us13 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul6 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein el13 (25 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul18 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein el31 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el19 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein us10 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein us12 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein el15 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein el40 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein us8 (14 kDa, Protein from Euglena gracilis)
- 18s rrna (747 kDa, RNA from Euglena gracilis)
- Ribosomal protein el33 (13 kDa, Protein from Euglena gracilis)
- 60s ribosomal protein l10 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein es26 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein el32 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul29 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul24 (16 kDa, Protein from Euglena gracilis)
- E-trna (24 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 7 (240 kDa, RNA from Euglena gracilis)
- Ribosomal protein us4 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein es10 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr2 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein el22 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein us2 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein us5 (27 kDa, Protein from Euglena gracilis)
- Ribosomal protein us17 (19 kDa, Protein from Euglena gracilis)
- 60s ribosomal protein l7a (32 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 2 (113 kDa, RNA from Euglena gracilis)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein us7 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul13 (24 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 3 (37 kDa, RNA from Euglena gracilis)
- Ribosomal protein el34 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul3 (46 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul30 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein el30 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul2 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein es19 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es24 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el37 (13 kDa, Protein from Euglena gracilis)
- P-trna (24 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 4 (225 kDa, RNA from Euglena gracilis)
- Ribosomal protein el29 (13 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 9 (52 kDa, RNA from Euglena gracilis)
- Ribosomal protein es21 (10 kDa, Protein from Euglena gracilis)
- Ribosomal protein es25 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein el20 (21 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 1 (42 kDa, RNA from Euglena gracilis)
- Ribosomal protein el27 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein el24 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el14 (25 kDa, Protein from Euglena gracilis)
- Ribosomal protein es28 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein el43 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein es17 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein el38 (9 kDa, Protein from Euglena gracilis)
- Ribosomal protein el41 (4 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 11 (30 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 13 (27 kDa, RNA from Euglena gracilis)
- A-trna (24 kDa, RNA from Euglena gracilis)
- Ribosomal protein es1 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr1 (7 kDa, Protein from Euglena gracilis)
- A-site trna (3 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 5 (170 kDa, RNA from Euglena gracilis)
- Rack1 (34 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul23 (18 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 6 (75 kDa, RNA from Euglena gracilis)
- Ribosomal protein el21 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein us15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein us11 (16 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 12 (18 kDa, RNA from Euglena gracilis)
- Ribosomal protein el18 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein es30 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein us14 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein us3 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein el42 (10 kDa, Protein from Euglena gracilis)
- Ribosomal protein es6 (31 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul5 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein es27 (9 kDa, Protein from Euglena gracilis)
- 5s rrna (38 kDa, RNA from Euglena gracilis)
- Ribosomal protein ul14 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul4 (41 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 8 (199 kDa, RNA from Euglena gracilis)
- Water (18 Da, Ligand)
- Ribosomal protein elegr3 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein us19 (17 kDa, Protein from Euglena gracilis)
- 5.8s rrna (52 kDa, RNA from Euglena gracilis)
- Euglena gracilis 80s ribosome (Complex from Euglena gracilis)
- Ribosomal protein eseug1 (32 kDa, Protein from Euglena gracilis)
- Ribosomal protein es8 (35 kDa, Protein from Euglena gracilis)
- Ribosomal protein es12 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein es7 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein us9 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el6 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein es4 (31 kDa, Protein from Euglena gracilis)
- Ribosomal protein el36 (12 kDa, Protein from Euglena gracilis)
Cryo-EM structure of of the large subunit of Leishmania ribosome bound to paromomycin
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 6az3
Q-score: 0.599
Shalev-Benami M, Zhang Y, Rozenberg H, Nobe Y, Taoka M, Matzov D, Zimmerman E, Bashan A, Isobe T, Jaffe CL, Yonath A, Skiniotis G
Nat Commun (2017) 8 pp. 1589-1589 [ DOI: doi:10.1038/s41467-017-01664-4 Pubmed: 29150609 ]
- Rrna beta (492 kDa, RNA from Leishmania donovani)
- Rrna alpha (575 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l23a, putative (13 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l18a (20 kDa, Protein from Leishmania donovani)
- Ribosomal protein el41 (4 kDa, Protein from Leishmania donovani)
- 60s_ribosomal_protein_l35_putative/genedb:lmjf.26.2330/genedb:lmjf.26.2340 (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l10, putative (24 kDa, Protein from Leishmania donovani)
- Ribosomal protein ul2 (27 kDa, Protein from Leishmania donovani)
- Ribosomal protein l15 (24 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l11 (l5, l16) (19 kDa, Protein from Leishmania donovani)
- Rrna epsilon (42 kDa, RNA from Leishmania donovani)
- Ribosomal protein ul24 (13 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l27a/l29, putative (16 kDa, Protein from Leishmania donovani)
- Rrna gamma (67 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l34, putative (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l23, putative (14 kDa, Protein from Leishmania donovani)
- Ribosomal l38e family protein (8 kDa, Protein from Leishmania donovani)
- Ribosomal protein ul3 (45 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l18, putative (21 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l37 (9 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l9, putative (21 kDa, Protein from Leishmania donovani)
- Ribosomal protein el24 (7 kDa, Protein from Leishmania donovani)
- Ribosomal protein el13 (23 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l39, putative (6 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l28, putative (15 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l21, putative (17 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l29 (7 kDa, Protein from Leishmania donovani)
- Ribosomal l27e family protein (15 kDa, Protein from Leishmania donovani)
- Water (18 Da, Ligand)
- Ribosomal protein ul13 (25 kDa, Protein from Leishmania donovani)
- 60s_ribosomal_protein_l32/genedb:lmjf.21.1720 (15 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l36, putative (11 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l37a (10 kDa, Protein from Leishmania donovani)
- Probable 60s ribosomal protein l14 (17 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l5, putative (34 kDa, Protein from Leishmania donovani)
- Rrna 5s (37 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l7a (39 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l7 family protein (26 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l30 (10 kDa, Protein from Leishmania donovani)
- Ubiquitin-60s ribosomal protein l40 (5 kDa, Protein from Leishmania donovani)
- 60s ribosomal protein l17, putative (17 kDa, Protein from Leishmania donovani)
- Rrna zeta (22 kDa, RNA from Leishmania donovani)
- 60s ribosomal protein l22, putative (14 kDa, Protein from Leishmania donovani)
- Paromomycin (615 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Ribosomal protein l19e family protein (22 kDa, Protein from Leishmania donovani)
- Ribosomal protein l1a, putative (40 kDa, Protein from Leishmania donovani)
- Rrna 5.8s (54 kDa, RNA from Leishmania donovani)
- Leishmania donovani 91s ribosome lsu (Complex from Leishmania donovani)
- 60s ribosomal protein l44, putative (11 kDa, Protein from Leishmania donovani)
- Rrna delta (59 kDa, RNA from Leishmania donovani)
- Ribosomal protein l35ae family protein (14 kDa, Protein from Leishmania donovani)
- 60s ribosomal subunit protein l31, putative (13 kDa, Protein from Leishmania donovani)
- Ribosomal protein el6 (21 kDa, Protein from Leishmania donovani)