Terminating ribosome with SRI-41315
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 8scb
Q-score: 0.589
Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S
Nat Chem Biol (2024) 20 pp. 877-884 [ DOI: doi:10.1038/s41589-023-01521-0 Pubmed: 38172604 ]
- El22 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l19 (23 kDa, Protein from Oryctolagus cuniculus)
- El42 (12 kDa, Protein from Oryctolagus cuniculus)
- 28s_rrna (1 MDa, RNA from Oryctolagus cuniculus)
- El35 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein s3 (26 kDa, Protein from Oryctolagus cuniculus)
- Es17 (15 kDa, Protein from Oryctolagus cuniculus)
- Es7 (22 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l10 (24 kDa, Protein from Oryctolagus cuniculus)
- Es28 (7 kDa, Protein from Oryctolagus cuniculus)
- Es31 (18 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l38 (8 kDa, Protein from Oryctolagus cuniculus)
- Us8 (14 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l23 (14 kDa, Protein from Oryctolagus cuniculus)
- Us15 (17 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s24 (15 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l18 (21 kDa, Protein from Oryctolagus cuniculus)
- Us4 (22 kDa, Protein from Oryctolagus cuniculus)
- Terminating rabbit ribosome (4 MDa, Complex from Oryctolagus cuniculus)
- 60s ribosomal protein l27 (15 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l12 (17 kDa, Protein from Oryctolagus cuniculus)
- Nc (13 kDa, Protein from Homo sapiens)
- El30 (12 kDa, Protein from Oryctolagus cuniculus)
- Us11 (18 kDa, Protein from Oryctolagus cuniculus)
- Us5 (31 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l29 (26 kDa, Protein from Oryctolagus cuniculus)
- El23 (17 kDa, Protein from Oryctolagus cuniculus)
- Receptor for activated c kinase 1 (rack1) (35 kDa, Protein from Oryctolagus cuniculus)
- Eukaryotic peptide chain release factor subunit 1 (51 kDa, Protein from Homo sapiens)
- El32 (15 kDa, Protein from Oryctolagus cuniculus)
- Es21 (9 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l37 (11 kDa, Protein from Oryctolagus cuniculus)
- El41 (3 kDa, Protein from Oryctolagus cuniculus)
- Mrna (63 kDa, RNA from Homo sapiens)
- Us12 (15 kDa, Protein from Oryctolagus cuniculus)
- El13 (24 kDa, Protein from Oryctolagus cuniculus)
- Us2 (sa) (32 kDa, Protein from Oryctolagus cuniculus)
- Es8 (24 kDa, Protein from Oryctolagus cuniculus)
- (2s,4as)-2-cyclobutyl-10-methyl-3-phenyl-2,10-dihydropyrimido[4,5-b]quinoline-4,5(3h,4ah)-dione (359 Da, Ligand)
- 60s ribosomal protein l34 (13 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l9 (21 kDa, Protein from Oryctolagus cuniculus)
- El21 (18 kDa, Protein from Oryctolagus cuniculus)
- Magnesium ion (24 Da, Ligand)
- El39 (6 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l11 (20 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l15 (24 kDa, Protein from Oryctolagus cuniculus)
- Iron/sulfur cluster (351 Da, Ligand)
- 60s ribosomal protein l7a (36 kDa, Protein from Oryctolagus cuniculus)
- Us17 (18 kDa, Protein from Oryctolagus cuniculus)
- Es12 (14 kDa, Protein from Oryctolagus cuniculus)
- 5.8s_rrna (50 kDa, RNA from Oryctolagus cuniculus)
- El28 (15 kDa, Protein from Oryctolagus cuniculus)
- Atp binding cassette subfamily e member 1 (67 kDa, Protein from Oryctolagus cuniculus)
- Es27 (9 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l14 (23 kDa, Protein from Oryctolagus cuniculus)
- Us9 (16 kDa, Protein from Oryctolagus cuniculus)
- El31 (14 kDa, Protein from Oryctolagus cuniculus)
- E_trna (24 kDa, RNA from Oryctolagus cuniculus)
- P_trna (24 kDa, RNA from Oryctolagus cuniculus)
- S10_plectin domain-containing protein (18 kDa, Protein from Oryctolagus cuniculus)
- Ul13 (23 kDa, Protein from Oryctolagus cuniculus)
- Ubiquitin a-52 residue ribosomal protein fusion product 1 (10 kDa, Protein from Oryctolagus cuniculus)
- 5s_rrna (38 kDa, RNA from Oryctolagus cuniculus)
- Us10 (13 kDa, Protein from Oryctolagus cuniculus)
- Us13 (17 kDa, Protein from Oryctolagus cuniculus)
- 18s_rrna (603 kDa, RNA from Oryctolagus cuniculus)
- 60s ribosomal protein l7 (29 kDa, Protein from Oryctolagus cuniculus)
- El33 (12 kDa, Protein from Oryctolagus cuniculus)
- 60s acidic ribosomal protein p0 (34 kDa, Protein from Oryctolagus cuniculus)
- Es6 (28 kDa, Protein from Oryctolagus cuniculus)
- El20 (20 kDa, Protein from Oryctolagus cuniculus)
- Zinc ion (65 Da, Ligand)
- Es30 (14 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l24 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l27a (16 kDa, Protein from Oryctolagus cuniculus)
- Es1 (30 kDa, Protein from Oryctolagus cuniculus)
- 40s ribosomal protein s26 (13 kDa, Protein from Oryctolagus cuniculus)
- Water (18 Da, Ligand)
- 60s ribosomal protein l6 (33 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l36 (12 kDa, Protein from Oryctolagus cuniculus)
- Ul24 (17 kDa, Protein from Oryctolagus cuniculus)
- 60s ribosomal protein l4 (46 kDa, Protein from Oryctolagus cuniculus)
- Ul22 (21 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l3 (46 kDa, Protein from Oryctolagus cuniculus)
- Es25 (13 kDa, Protein from Oryctolagus cuniculus)
- Us14 (6 kDa, Protein from Oryctolagus cuniculus)
- El43 (10 kDa, Protein from Oryctolagus cuniculus)
- Es4 (s4 x isoform) (29 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal protein l8 (28 kDa, Protein from Oryctolagus cuniculus)
- Us19 (17 kDa, Protein from Oryctolagus cuniculus)
- Us7 (22 kDa, Protein from Oryctolagus cuniculus)
- Es19 (16 kDa, Protein from Oryctolagus cuniculus)
- Ribosomal_l18_c domain-containing protein (34 kDa, Protein from Oryctolagus cuniculus)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 7m5d
Q-score: 0.526
To Be Published
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- E.coli 70s ribosome in complex with rf3-gtp, rf1 and p-trna (state i) (Complex from Escherichia coli)
- 50s ribosomal protein l17 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- Mrna (4 kDa, RNA from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- Peptide chain release factor 1 (40 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Cryo-em structure of a non-rotated e.coli 70s ribosome in complex with rf3-gtp, rf1 and p-trna (state i) (Complex)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- Mrna (Complex from Escherichia coli)
- 30s ribosomal protein s19 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l11 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- P-trna (24 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l27 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (25 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s11 (12 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- Peptide chain release factor 3 (58 kDa, Protein from Escherichia coli)
- Fme-phe-phe (471 Da, Protein from Escherichia coli)
- 16s ribosomal rna (497 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l10 (14 kDa, Protein from Escherichia coli)
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 us19 (17 kDa, Protein from Euglena gracilis)
- 60s ribosomal protein l7a (32 kDa, Protein from Euglena gracilis)
- Ribosomal protein es4 (31 kDa, Protein from Euglena gracilis)
- Ribosomal protein es31 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein us14 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein es26 (13 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 13 (27 kDa, RNA from Euglena gracilis)
- Ribosomal protein el21 (18 kDa, Protein from Euglena gracilis)
- Zinc ion (65 Da, Ligand)
- Ribosomal protein el34 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein el32 (16 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 10 (20 kDa, RNA from Euglena gracilis)
- A-site trna (3 kDa, RNA from Euglena gracilis)
- Ribosomal protein es7 (22 kDa, Protein from Euglena gracilis)
- 60s ribosomal protein l10 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein us17 (19 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul18 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein el6 (22 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 5 (170 kDa, RNA from Euglena gracilis)
- Ribosomal protein el41 (4 kDa, Protein from Euglena gracilis)
- E-trna (24 kDa, RNA from Euglena gracilis)
- 5.8s rrna (52 kDa, RNA from Euglena gracilis)
- Ribosomal protein el38 (9 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 4 (225 kDa, RNA from Euglena gracilis)
- Ribosomal protein es12 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul24 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul5 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein el20 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein el36 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein es30 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein us3 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul4 (41 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul29 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein el31 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein us15 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein es17 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es19 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein es8 (35 kDa, Protein from Euglena gracilis)
- Ribosomal protein es27 (9 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 8 (199 kDa, RNA from Euglena gracilis)
- Ribosomal protein el18 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein el37 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein us12 (15 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 6 (75 kDa, RNA from Euglena gracilis)
- Ribosomal protein es1 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein el29 (13 kDa, Protein from Euglena gracilis)
- Rack1 (34 kDa, Protein from Euglena gracilis)
- Ribosomal protein el33 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul30 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein us8 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein us7 (21 kDa, Protein from Euglena gracilis)
- Ribosomal protein el19 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein us13 (17 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 9 (52 kDa, RNA from Euglena gracilis)
- Ribosomal protein es24 (16 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 11 (30 kDa, RNA from Euglena gracilis)
- A-trna (24 kDa, RNA from Euglena gracilis)
- Ribosomal protein us10 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein eseug1 (32 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul23 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein el14 (25 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul2 (28 kDa, Protein from Euglena gracilis)
- Ribosomal protein el40 (14 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 7 (240 kDa, RNA from Euglena gracilis)
- Lsu rrna chain 2 (113 kDa, RNA from Euglena gracilis)
- Ribosomal protein el30 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein es10 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein el22 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein el13 (25 kDa, Protein from Euglena gracilis)
- 5s rrna (38 kDa, RNA from Euglena gracilis)
- Ribosomal protein ul3 (46 kDa, Protein from Euglena gracilis)
- Ribosomal protein es6 (31 kDa, Protein from Euglena gracilis)
- Ribosomal protein el15 (24 kDa, Protein from Euglena gracilis)
- Ribosomal protein el39 (6 kDa, Protein from Euglena gracilis)
- Ribosomal protein es21 (10 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 3 (37 kDa, RNA from Euglena gracilis)
- Ribosomal protein elegr1 (7 kDa, Protein from Euglena gracilis)
- Euglena gracilis 80s ribosome (Complex from Euglena gracilis)
- Ribosomal protein ul13 (24 kDa, Protein from Euglena gracilis)
- P-trna (24 kDa, RNA from Euglena gracilis)
- Ribosomal protein us9 (17 kDa, Protein from Euglena gracilis)
- Ribosomal protein us2 (29 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul22 (18 kDa, Protein from Euglena gracilis)
- Ribosomal protein us11 (16 kDa, Protein from Euglena gracilis)
- Ribosomal protein el42 (10 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 1 (42 kDa, RNA from Euglena gracilis)
- Water (18 Da, Ligand)
- Ribosomal protein el27 (15 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr2 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein el24 (17 kDa, Protein from Euglena gracilis)
- Lsu rrna chain 12 (18 kDa, RNA from Euglena gracilis)
- Ribosomal protein us5 (27 kDa, Protein from Euglena gracilis)
- Ribosomal protein el43 (12 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul6 (22 kDa, Protein from Euglena gracilis)
- Ribosomal protein elegr3 (7 kDa, Protein from Euglena gracilis)
- Ribosomal protein es25 (13 kDa, Protein from Euglena gracilis)
- Ribosomal protein ul14 (14 kDa, Protein from Euglena gracilis)
- Ribosomal protein es28 (8 kDa, Protein from Euglena gracilis)
- Ribosomal protein us4 (22 kDa, Protein from Euglena gracilis)
- 18s rrna (747 kDa, RNA from Euglena gracilis)