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 [ Pubmed: 34029205 DOI: doi:10.1126/science.abf3546 ]
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el13 (24 kDa, Protein from Oryctolagus cuniculus)
- Sars-cov-2 pseudoknot (Complex from Severe acute respiratory syndrome coronavirus 2)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s7 (47 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3a (30 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s11 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l26 (17 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Bos taurus)
- 40s ribosomal protein s18 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l41 (3 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- 5s rrna (38 kDa, RNA from Oryctolagus cuniculus)
- Ul29 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us11 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s8 (24 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l13a (23 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es21 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el28 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul2 (28 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18a (20 kDa, Protein from Oryctolagus cuniculus)
- Spermidine (145 Da, Ligand)
- Ribosomal protein s28 (7 kDa, Protein from Oryctolagus cuniculus)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- El24 (17 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s9 (predicted) (22 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s12 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es4 (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul30 (29 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (121 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 5.8s rrna (50 kDa, RNA from Oryctolagus cuniculus)
- 40s ribosomal protein es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein es19 (16 kDa, Protein from Oryctolagus cuniculus)
- Edf1 (16 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome stalled by the sars-cov-2 pseudoknot (Complex)
- 40s ribosomal protein s30 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el22 (14 kDa, Protein from Oryctolagus cuniculus)
- P-site trna(pro) (24 kDa, RNA from Bos taurus)
- 40s ribosomal protein s25 (13 kDa, Protein from Oryctolagus cuniculus)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- Replicase polyprotein 1ab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ribosomal protein es26 (13 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s6 (28 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s27a (18 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s5 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s15a (14 kDa, Protein from Oryctolagus cuniculus)
- Unknown atom or ion (Ligand)
- 40s ribosomal protein s23 (15 kDa, Protein from Oryctolagus cuniculus)
- Rabbit 80s ribosome colliding in another ribosome (Complex from Oryctolagus cuniculus)
- Ribosomal protein es10 (18 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein sa (32 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s3 (31 kDa, Protein from Oryctolagus cuniculus)
- A-site met-trna(met) (24 kDa, RNA from Bos taurus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Us9 (19 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us10 (13 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein us5 (31 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein ul1 (24 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein el8 (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein us19 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s27 (9 kDa, Protein from Oryctolagus cuniculus)
- 28s rrna (1 MDa, RNA from Oryctolagus cuniculus)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- Rack1 (35 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l40 (14 kDa, Protein from Oryctolagus cuniculus)
- Mrna containing sars-cov-2 sequence (69 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Ul23 (17 kDa, Protein from Oryctolagus cuniculus)
- El38 (8 kDa, Protein from Oryctolagus cuniculus)
- 18s rrna (603 kDa, RNA from Oryctolagus cuniculus)
Cryo-EM reconstruction of the 70S chloroplast ribosome
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 5mmm
Q-score: 0.406
Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N
EMBO J (2017) 36 pp. 475-486 [ Pubmed: 28007896 DOI: doi:10.15252/embj.201695959 ]
- Plastid ribosomal protein us10c (21 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein 6, chloroplastic (12 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s7, chloroplastic (17 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s3, chloroplastic (24 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul15c (29 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul6c (24 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein cl37, psrp5 (15 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s19 alpha, chloroplastic (10 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l32, chloroplastic (6 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s4, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- 16s ribosomal rna (483 kDa, RNA from Spinacia oleracea)
- Plastid ribosomal protein ul4c (32 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s14, chloroplastic (11 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l34, chloroplastic (16 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein us17c (18 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l2, chloroplastic (29 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l11, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s16, chloroplastic (10 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein 3, chloroplastic (20 kDa, Protein from Spinacia oleracea)
- Ribosome-binding factor psrp1, chloroplastic (33 kDa, Protein from Spinacia oleracea)
- Trna-phe (24 kDa, RNA from Spinacia oleracea)
- Plastid ribosomal protein us13c (19 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bl27c (21 kDa, Protein from Spinacia oleracea)
- 23s ribosomal rna (911 kDa, RNA from Spinacia oleracea)
- Plastid ribosomal protein ul5c (28 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l35, chloroplastic (17 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l22, chloroplastic (23 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s8, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l16, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s31, chloroplastic (10 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l36, chloroplastic (4 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein us9c (22 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s11, chloroplastic (14 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bs21c (20 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l14, chloroplastic (13 kDa, Protein from Spinacia oleracea)
- 4.5s ribosomal rna (34 kDa, RNA from Spinacia oleracea)
- 30s ribosomal protein s2, chloroplastic (26 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s15, chloroplastic (10 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bs20c (20 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bl28c (16 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bl9c (22 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul14c (14 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul10c (26 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s18, chloroplastic (12 kDa, Protein from Spinacia oleracea)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l20, chloroplastic (15 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l31 (14 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bs6c (23 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul3c (33 kDa, Protein from Spinacia oleracea)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein 2, chloroplastic (28 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l21, chloroplastic (28 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s12, chloroplastic (13 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein bs1c (14 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l33, chloroplastic (7 kDa, Protein from Spinacia oleracea)
- 30s ribosomal protein s5, chloroplastic (33 kDa, Protein from Spinacia oleracea)
- Chloroplast 70s ribosome (2 MDa, Complex from Spinacia oleracea)
- Plastid ribosomal protein ul24c (21 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul29c (19 kDa, Protein from Spinacia oleracea)
- 5s ribosomal rna (39 kDa, RNA from Spinacia oleracea)
- 50s ribosomal protein l19, chloroplastic (26 kDa, Protein from Spinacia oleracea)
- Plastid ribosomal protein ul18c (18 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l23, chloroplastic (21 kDa, Protein from Spinacia oleracea)
- 50s ribosomal protein l13, chloroplastic (28 kDa, Protein from Spinacia oleracea)