Electron Microscopy Data Bank

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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

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)

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EMD-27880

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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

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)

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EMD-27881

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E. coli 50S ribosome bound to antibiotic analog SLC21

Release date: June 28, 2023
Resolution: 2.32 Å
EM Method: Single-particle
Fitted PDBs: 8e46
Q-score: 0.609

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)
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)
(2r,3s,4r,5r,8r,10r,11r,12s,13s,14r)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-({3,4,6-trideoxy-3-[{[1-(2-{[(1r,2r)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]amino}-2-oxoethyl)-1h-1,2,3-triazol-4-yl]methyl}(methyl)amino]-beta-d-xylo-hexopyranosyl}oxy)-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-c-methyl-3-o-methyl-alpha-l-ribo-hexopyranoside (1 kDa, Ligand)
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)

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EMD-27882

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E. coli 50S ribosome bound to antibiotic analog SLC26

Release date: June 28, 2023
Resolution: 2.32 Å
EM Method: Single-particle
Fitted PDBs: 8e47
Q-score: 0.604

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)
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)
(2r,3s,4r,5r,8r,10r,11r,12s,13s,14r)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-({3,4,6-trideoxy-3-[(2-{[2-({[(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}amino)-2-oxoethyl]sulfanyl}ethyl)(methyl)amino]-beta-d-xylo-hexopyranosyl}oxy)-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-c-methyl-3-o-methyl-alpha-l-ribo-hexopyranoside (1 kDa, 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)

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EMD-27883

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E. coli 50S ribosome bound to antibiotic analog SLC30

Release date: June 28, 2023
Resolution: 2.27 Å
EM Method: Single-particle
Fitted PDBs: 8e48
Q-score: 0.566

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~{s},3~{s},4~{r},6~{r})-4-[[2-[[(5~{s})-3-[3-fluoranyl-4-[6-(2-methyl-1,2,3,4-tetrazol-5-yl)pyridin-3-yl]phenyl]-2-oxidanylidene-1,3-oxazolidin-5-yl]methylamino]-2-oxidanylidene-ethyl]-methyl-amino]-6-methyl-2-(phenylcarbonyloxy)oxan-3-yl] benzoate (778 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)

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EMD-27884

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E. coli 50S ribosome bound to antibiotic analog SLC31

Release date: June 28, 2023
Resolution: 2.05 Å
EM Method: Single-particle
Fitted PDBs: 8e49
Q-score: 0.628

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)
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)
~{n}-[[(5~{s})-3-[3-fluoranyl-4-[6-(2-methyl-1,2,3,4-tetrazol-5-yl)pyridin-3-yl]phenyl]-2-oxidanylidene-1,3-oxazolidin-5-yl]methyl]-2-[methyl-[(2~{r},3~{r},4~{s},6~{r})-6-methyl-2,3-bis(oxidanyl)oxan-4-yl]amino]ethanamide (570 Da, Ligand)

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