E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state
Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T
Nat Struct Mol Biol (2024) 31 pp. 817-825 [ DOI: doi:10.1038/s41594-024-01238-1 Pubmed: 38538915 ]
- A-, p- site trna (Complex from Escherichia coli BW25113)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (Complex from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- A-site trna_ile2 (24 kDa, RNA from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- Mrna (15 kDa, RNA from Escherichia coli)
- Mrna (Complex)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- The complex of e. coli 70s ribosome with mrna and a-, p- site trna (Complex)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- P-site trna_glu (24 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 8htz
Q-score: 0.657
Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T
Nat Struct Mol Biol (2024) 31 pp. 817-825 [ Pubmed: 38538915 DOI: doi:10.1038/s41594-024-01238-1 ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- A-site trna (Complex from Haloarcula marismortui)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (Complex from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Mrna (15 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (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)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- P-site trna_glu (24 kDa, RNA from Escherichia coli BW25113)
- Mrna (Complex)
- A-site trna_ile2 (25 kDa, RNA from Haloarcula marismortui)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- The complex of e. coli 70s ribosome with mrna and a-, p- site trna (Complex)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- P-site trna (Complex from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and ct6A37 in classical state
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 8hu1
Q-score: 0.599
Akiyama N, Ishiguro K, Yokoyama T, Miyauchi K, Nagao A, Shirouzu M, Suzuki T
Nat Struct Mol Biol (2024) 31 pp. 817-825 [ Pubmed: 38538915 DOI: doi:10.1038/s41594-024-01238-1 ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- E. coli 70s ribosome (Complex from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- Mrna (15 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (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)
- A-site trna_ile2 (24 kDa, RNA from Escherichia coli BW25113)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- P-site trna_glu (24 kDa, RNA from Escherichia coli BW25113)
- Mrna (Complex)
- Potassium ion (39 Da, Ligand)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- The complex of e. coli 70s ribosome with mrna and a-, p- site trna (Complex)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6, fully modified isoform (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- Trna (Complex from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
Streptomycin and Hygromycin B bound to the 30S body
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 8cai
Q-score: 0.698
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- Spectinomycin (332 Da, Ligand)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Hygromycin b variant (527 Da, Ligand)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- [(2~{s},3~{s},4~{s},5~{r},6~{s})-2-[(2~{r},3~{r},4~{r},5~{s})-2-[(1~{r},2~{s},3~{r},4~{r},5~{s},6~{r})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium (602 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
Streptomycin bound to the 30S body
Resolution: 1.79 Å
EM Method: Single-particle
Fitted PDBs: 8cgj
Q-score: 0.729
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Tetracycline (444 Da, Ligand)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein us3 (26 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- [(2~{s},3~{s},4~{s},5~{r},6~{s})-2-[(2~{r},3~{r},4~{r},5~{s})-2-[(1~{r},2~{s},3~{r},4~{r},5~{s},6~{r})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium (602 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Apramycin bound to the 30S body
Resolution: 2.12 Å
EM Method: Single-particle
Fitted PDBs: 8cgr
Q-score: 0.722
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- Apramycin (539 Da, Ligand)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Gentamicin bound to the 30S body
Resolution: 1.89 Å
EM Method: Single-particle
Fitted PDBs: 8cgu
Q-score: 0.76
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ Pubmed: 37550453 DOI: doi:10.1038/s41594-023-01047-y ]
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Potassium ion (39 Da, Ligand)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- (2r,3r,4r,5r)-2-((1s,2s,3r,4s,6r)-4,6-diamino-3-((2r,3r,6s)-3-amino-6-(aminomethyl)-tetrahydro-2h-pyran-2-yloxy)-2-hydr oxycyclohexyloxy)-5-methyl-4-(methylamino)-tetrahydro-2h-pyran-3,5-diol (449 Da, Ligand)
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
Kasugamycin bound to the 30S body
Resolution: 2.04 Å
EM Method: Single-particle
Fitted PDBs: 8cep
Q-score: 0.734
Paternoga H, Crowe-McAuliffe C, Bock LV, Koller TO, Morici M, Beckert B, Myasnikov AG, Grubmuller H, Novacek J, Wilson DN
Nat Struct Mol Biol (2023) 30 pp. 1380-1392 [ DOI: doi:10.1038/s41594-023-01047-y Pubmed: 37550453 ]
- Small ribosomal subunit protein bs21 (8 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein bs6, non-modified isoform (15 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us11 (13 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us15 (10 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us5 (17 kDa, Protein from Escherichia coli BW25113)
- (1s,2r,3s,4r,5s,6s)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-4-{[carboxy(imino)methyl]amino}-2,3,4,6-tetradeoxy-alpha-d-arabino-hexopyranoside (379 Da, Ligand)
- Potassium ion (39 Da, Ligand)
- 70s ribosomes with antibiotic cocktail (Complex from Escherichia coli BW25113)
- Small ribosomal subunit protein bs18 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us4 (23 kDa, Protein from Escherichia coli BW25113)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli BW25113)
- 23s rrna (941 kDa, RNA from Escherichia coli BW25113)
- Water (18 Da, Ligand)
- Capreomycin ia (686 Da, Protein from Streptomyces californicus)
- Small ribosomal subunit protein us17 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us12 (13 kDa, Protein from Escherichia coli BW25113)
- Magnesium ion (24 Da, Ligand)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli BW25113)
- Small ribosomal subunit protein us8 (14 kDa, Protein from Escherichia coli BW25113)
- 16s rrna (499 kDa, RNA from Escherichia coli BW25113)
Wild-type Escherichia coli ribosome with antibiotic radezolid
Resolution: 2.47 Å
EM Method: Single-particle
Fitted PDBs: 7s1j
Q-score: 0.552
Tsai K, Stojkovic V, Lee DJ, Young ID, Szal T, Klepacki D, Vazquez-Laslop N, Mankin AS, Fraser JS, Fujimori DG
Nat Struct Mol Biol (2022) 29 pp. 162-171 [ DOI: doi:10.1038/s41594-022-00723-9 Pubmed: 35165456 ]
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s21 (8 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s5 (17 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l36 (4 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- Wild-type escherichia coli ribosome with antibiotic radezolid (2 MDa, Complex from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s20 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- Radezolid (438 Da, Ligand)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 23s rrna (941 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 16s rrna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 5s rrna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)