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sample_name:"23S Ribosomal RNA" AND release_date:[2023-01-01T00:00:00Z TO 2023-12-31T23:59:59Z] AND natural_source_ncbi_code:"562"
Release date: Aug. 9, 2023
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8syl
Q-score: 0.544
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8syl
Q-score: 0.544
Seely SM, Parajuli NP, De Tarafder A, Ge X, Sanyal S, Gagnon MG
Nat Commun (2023) 14 pp. 4666-4666 [ DOI: doi:10.1038/s41467-023-40416-5 Pubmed: 37537169 ]
Sample:
- 30s ribosomal protein s10 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l20 (13 kDa, Protein from Escherichia coli)
- Phenylalanine trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s17 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l23 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- (2s)-n-[(1r,2s,3s,4r,5s)-4-[(2r,3r,4s,5s,6r)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2s,3r,4s,5s ,6r)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide (585 Da, Ligand)
- 30s ribosomal protein s11 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s5 (17 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 l36 (4 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l15 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s2 (26 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s12 (13 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s19 (10 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l14 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l27 (9 kDa, Protein from Escherichia coli)
- Ribosomal protein l21 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Escherichia coli 70s ribosome in complex with amikacin, mrna, and a-, p-, and e-site trnas (2 MDa, Complex from Escherichia coli)
- 50s ribosomal protein l5 (20 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l17 (14 kDa, Protein from Escherichia coli)
- Phenylalanine (165 Da, Ligand)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l28 (9 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l9 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l18 (12 kDa, Protein from Escherichia coli)
- Zinc ion (65 Da, Ligand)
- 30s ribosomal protein s18 (9 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s6 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l24 (11 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 16s ribosomal rna (499 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l19 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l35 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s9 (14 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s4 (23 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l33 (6 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 30s ribosomal protein s14 (11 kDa, Protein from Escherichia coli)
- Magnesium ion (24 Da, Ligand)
- 50s ribosomal protein l6 (18 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- M-f-stop mrna (7 kDa, RNA from Escherichia phage T4)
- 50s ribosomal protein l31 (7 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s15 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s13 (13 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l30 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l25 (10 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s7 (17 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s3 (26 kDa, Protein from Escherichia coli)
- P-site initiator trna (24 kDa, RNA from Escherichia coli)
- 30s ribosomal protein s8 (14 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l29 (7 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l16 (15 kDa, Protein from Escherichia coli)
- 30s ribosomal protein s16 (9 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin A analog 3142
Release date: June 28, 2023
Resolution: 1.91 Å
EM Method: Single-particle
Fitted PDBs: 8e30
Q-score: 0.629
Resolution: 1.91 Å
EM Method: Single-particle
Fitted PDBs: 8e30
Q-score: 0.629
Li Q, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- N-{2-[4-(aminomethyl)-1h-1,2,3-triazol-1-yl]ethyl}-2-[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-4-yl]acetamide (698 Da, Ligand)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin analogs SA1 and SB1
Release date: June 28, 2023
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e32
Q-score: 0.609
Resolution: 2.35 Å
EM Method: Single-particle
Fitted PDBs: 8e32
Q-score: 0.609
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- (3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-yn-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,7h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione (555 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- ~{n}-[(3~{s},6~{s},12~{r},15~{s},16~{r},19~{s},22~{s},24~{r})-12-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethyl]-4,16-dimethyl-24-oxidanyl-2,5,11,14,18,21-hexakis(oxidanylidene)-19-phenyl-3-(phenylmethyl)-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide (867 Da, Ligand)
E. coli 50S ribosome bound to compound streptogramin analog SAB001
Release date: June 28, 2023
Resolution: 2.23 Å
EM Method: Single-particle
Fitted PDBs: 8e33
Q-score: 0.602
Resolution: 2.23 Å
EM Method: Single-particle
Fitted PDBs: 8e33
Q-score: 0.602
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- N-{(4r,6r,9s,10r,13s,15as,17r,20r,22s,24as)-22-benzyl-6-[2-(4-{[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-4-yl]methyl}-1h-1,2,3-triazol-1-yl)ethyl]-17-hydroxy-10,23-dimethyl-5,8,12,15,21,24-hexaoxo-13-phenyldocosahydro-12h-pyrido[2,1-f]pyrrolo[2,1-l][1,4,7,10,13,16]oxapentaazacyclononadecin-9-yl}-3-hydroxypyridine-2-carboxamide (1 kDa, Ligand)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound SAB002
Release date: June 28, 2023
Resolution: 2.27 Å
EM Method: Single-particle
Fitted PDBs: 8e35
Q-score: 0.569
Resolution: 2.27 Å
EM Method: Single-particle
Fitted PDBs: 8e35
Q-score: 0.569
Takahashi Y, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- N-{(4r,6r,9s,10r,13s,15as,17r,20r,22s,24as)-22-benzyl-6-[3-(4-{[(3r,4r,5e,10e,12e,14s,16r,23r,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-4-yl]methyl}-1h-1,2,3-triazol-1-yl)propyl]-17-hydroxy-10,23-dimethyl-5,8,12,15,21,24-hexaoxo-13-phenyldocosahydro-12h-pyrido[2,1-f]pyrrolo[2,1-l][1,4,7,10,13,16]oxapentaazacyclononadecin-9-yl}-3-hydroxypyridine-2-carboxamide (1 kDa, Ligand)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- Water (18 Da, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 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 l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin A analog 3146
Release date: June 28, 2023
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8e36
Q-score: 0.57
Resolution: 2.38 Å
EM Method: Single-particle
Fitted PDBs: 8e36
Q-score: 0.57
Li Q, Pellegrino J, Lee DJ, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 2-[(3r,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-3-(propan-2-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-4-yl]-n-{2-[4-(pyridin-4-yl)-1h-1,2,3-triazol-1-yl]ethyl}acetamide (746 Da, Ligand)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 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 l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to solithromycin and VM1
Release date: June 28, 2023
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 8e3o
Q-score: 0.618
Resolution: 1.99 Å
EM Method: Single-particle
Fitted PDBs: 8e3o
Q-score: 0.618
Boyce JH, Pellegrino J, Lee DJ, Ecker AK, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- Virginiamycin m1 (525 Da, Ligand)
- (3as,4r,7s,9r,10r,11r,13r,15r,15ar)-1-{4-[4-(3-aminophenyl)-1h-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2h-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-d-xylo-hexopyranoside (845 Da, Ligand)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to compound streptogramin A analog 3336
Release date: June 28, 2023
Resolution: 2.09 Å
EM Method: Single-particle
Fitted PDBs: 8e43
Q-score: 0.602
Resolution: 2.09 Å
EM Method: Single-particle
Fitted PDBs: 8e43
Q-score: 0.602
Li Q, Pellegrino J, Lee DJ, Fraser JS, Seiple IB
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- (2r)-2-[(3s,4r,5e,10e,12e,14s,16r,23s,26ar)-16-fluoro-14-hydroxy-12-methyl-1,7,22-trioxo-4-(prop-2-en-1-yl)-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1h,3h,22h-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate (743 Da, Ligand)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 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 l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to antibiotic analog SLC09
Release date: June 28, 2023
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8e44
Q-score: 0.582
Resolution: 2.53 Å
EM Method: Single-particle
Fitted PDBs: 8e44
Q-score: 0.582
Yeon SK, Pellegrino J, Lee DJ, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l15 (15 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l32 (6 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)
- 2-chloro-n-{[(5s)-3-{(4m)-3-fluoro-4-[(6p)-6-(2-methyl-2h-tetrazol-5-yl)pyridin-3-yl]phenyl}-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide (445 Da, Ligand)
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l2 (29 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
E. coli 50S ribosome bound to antibiotic analog SLC17
Release date: June 28, 2023
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8e45
Q-score: 0.612
Resolution: 2.3 Å
EM Method: Single-particle
Fitted PDBs: 8e45
Q-score: 0.612
Yeon SK, Pellegrino J, Lee DJ, Seiple IB, Fraser JS
To Be Published
Sample:
- 50s ribosomal protein l22 (12 kDa, Protein from Escherichia coli)
- 23s ribosomal rna (941 kDa, RNA from Escherichia coli)
- 50s e. coli ribosome (Complex from Escherichia coli)
- 50s ribosomal protein l3 (22 kDa, Protein from Escherichia coli)
- 2-{[(2s,3r,4s,6r)-2-{[(2r,3s,4r,5r,8r,10r,11r,12s,13s,14r)-2-ethyl-3,4,10-trihydroxy-13-{[(2r,4r,5s,6s)-5-hydroxy-4-methoxy-4,6-dimethyloxan-2-yl]oxy}-3,5,6,8,10,12,14-heptamethyl-15-oxo-1-oxa-6-azacyclopentadecan-11-yl]oxy}-3-hydroxy-6-methyloxan-4-yl](methyl)amino}-n-{[(5s)-3-{(4m)-3-fluoro-4-[(6p)-6-(2-methyl-2h-tetrazol-5-yl)pyridin-3-yl]phenyl}-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide (non-preferred name) (1 kDa, Ligand)
- 50s ribosomal protein l13 (16 kDa, Protein from Escherichia coli)
- 50s ribosomal protein l4 (22 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 l2 (29 kDa, Protein from Escherichia coli)
- 5s ribosomal rna (38 kDa, RNA from Escherichia coli)
- 50s ribosomal protein l34 (5 kDa, Protein from Escherichia coli)