Equivalence class NR_2.5_10157.114 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4YBB|1|DB (rep) | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2015-03-18 |
| 2 | 4YBB|1|CB | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2015-03-18 |
| 3 | 8B0X|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli B | Bacteria | RF00001 | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | Electron microscopy | 1.55 | 2022-11-30 |
| 4 | 8AYE|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | Electron microscopy | 1.96 | 2023-03-01 |
| 5 | 7K00|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | Electron microscopy | 1.98 | 2020-09-23 |
| 6 | 8G6W|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe | Electron microscopy | 2.02 | 2023-04-05 |
| 7 | 8G6Y|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe | Electron microscopy | 2.09 | 2023-04-05 |
| 8 | 8EMM|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates | Electron microscopy | 2.1 | 2023-05-31 |
| 9 | 8ANA|1|b | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00001 | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit | Electron microscopy | 2.1 | 2023-03-08 |
| 10 | 6XZ7|1|B | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | Electron microscopy | 2.1 | 2020-07-22 |
| 11 | 7QQ3|1|J | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli K-12 | Bacteria | RF00001 | Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. | Electron microscopy | 2.1 | 2023-01-18 |
| 12 | 7ZP8|1|a | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | 70S E. coli ribosome with a stalled filamin domain 5 nascent chain | Electron microscopy | 2.2 | 2022-08-10 |
| 13 | 8EIU|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | Electron microscopy | 2.24 | 2023-02-01 |
| 14 | 7LVK|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Cfr-modified 50S subunit from Escherichia coli | Electron microscopy | 2.2 | 2021-12-15 |
| 15 | 6PJ6|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | High resolution cryo-EM structure of E.coli 50S | Electron microscopy | 2.2 | 2020-01-22 |
| 16 | 7N1P|1|5 | 5S ribosomal RNA | 5S rRNA | Escherichia coli K-12 | Bacteria | RF00001 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | Electron microscopy | 2.33 | 2021-07-14 |
| 17 | 8AKN|1|b | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00001 | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | Electron microscopy | 2.3 | 2023-03-08 |
| 18 | 8G6X|1|b | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site meta-aminobenzoic acid charged NH-tRNAPhe | Electron microscopy | 2.31 | 2023-03-22 |
| 19 | 7PJS|1|B | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli | Bacteria | RF00001 | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | Electron microscopy | 2.35 | 2021-10-20 |
| 20 | 7Z20|1|a | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | Electron microscopy | 2.29 | 2022-08-10 |
| 21 | 7O1A|1|BB | 5S ribosomal RNA | Ribosomal RNA 5S | Escherichia coli K-12 | Bacteria | RF00001 | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | Electron microscopy | 2.4 | 2021-09-01 |
| 22 | 7S1H|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Wild-type Escherichia coli ribosome with antibiotic linezolid | Electron microscopy | 2.35 | 2021-11-17 |
| 23 | 7S1K|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.42 | 2022-01-19 |
| 24 | 7BL4|1|B | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli K-12 | Bacteria | RF00001 | in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle | Electron microscopy | 2.4 | 2021-05-12 |
| 25 | 7S1J|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Wild-type Escherichia coli ribosome with antibiotic radezolid | Electron microscopy | 2.47 | 2022-03-02 |
| 26 | 7S1G|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | Electron microscopy | 2.48 | 2021-11-17 |
| 27 | 7S1I|1|J | 5S ribosomal RNA | 5S rRNA | Escherichia coli | Bacteria | RF00001 | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.48 | 2022-03-02 |
| 28 | 6PC6|1|J | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli | Bacteria | RF00001 | E. coli 50S ribosome bound to compound 47 | Electron microscopy | 2.5 | 2020-06-17 |
| 29 | 6PCR|1|J | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli | Bacteria | RF00001 | E. coli 50S ribosome bound to compound 40o | Electron microscopy | 2.5 | 2020-06-17 |
| 30 | 6PC7|1|J | 5S ribosomal RNA | 5S ribosomal RNA | Escherichia coli | Bacteria | RF00001 | E. coli 50S ribosome bound to compound 46 | Electron microscopy | 2.5 | 2020-06-17 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_10157.114 | NR_2.5_10157.113 | 3.285 | (29) 7S1G|1|J, 7QQ3|1|J, 7PJS|1|B, 7O1A|1|BB, 7N1P|1|5, 7LVK|1|J, 7K00|1|b, 7BL4|1|B, 6XZ7|1|B, 6PJ6|1|J, 6PCR|1|J, 6PC7|1|J, 6PC6|1|J, 4YBB|1|DB, 4YBB|1|CB, 8G6Y|1|b, 8G6X|1|b, 8G6W|1|b, 8EIU|1|b, 8B0X|1|b, 8AYE|1|b, 8ANA|1|b, 8AKN|1|b, 7ZP8|1|a, 7Z20|1|a, 7S1K|1|J, 7S1J|1|J, 7S1I|1|J, 7S1H|1|J | (1) 8EMM|1|b | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_10157.114 | NR_2.5_10157.115 | 3.289 | (30) 7PJS|1|B, 8AYE|1|b, 7BL4|1|B, 7S1K|1|J, 8G6Y|1|b, 6PC6|1|J, 7QQ3|1|J, 8B0X|1|b, 7K00|1|b, 7Z20|1|a, 6PC7|1|J, 7S1G|1|J, 8EIU|1|b, 7LVK|1|J, 7ZP8|1|a, 6PCR|1|J, 7S1H|1|J, 8EMM|1|b, 7N1P|1|5, 8AKN|1|b, 6PJ6|1|J, 7S1I|1|J, 8G6W|1|b, 4YBB|1|CB, 7O1A|1|BB, 8ANA|1|b, 6XZ7|1|B, 7S1J|1|J, 8G6X|1|b, 4YBB|1|DB | (0) | (16) 8E3L|1|J, 8E3M|1|J, 8E36|1|J, 8E35|1|J, 8E33|1|J, 8E32|1|J, 8E30|1|J, 8E49|1|J, 8E48|1|J, 8E47|1|J, 8E46|1|J, 8E45|1|J, 8E43|1|J, 8E42|1|J, 8E41|1|J, 8E3O|1|J |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5
#S - ordering by similarity (same as in the heat map).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 7PJS|1|B | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | ELECTRON MICROSCOPY | 2.35 | 120 |
| 2 | 7LVK|1|J | Cfr-modified 50S subunit from Escherichia coli | ELECTRON MICROSCOPY | 2.2 | 118 |
| 3 | 6PJ6|1|J | High resolution cryo-EM structure of E.coli 50S | ELECTRON MICROSCOPY | 2.2 | 118 |
| 4 | 4YBB|1|CB | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 118 |
| 5 | 4YBB|1|DB | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 120 |
| 6 | 6XZ7|1|B | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | ELECTRON MICROSCOPY | 2.1 | 120 |
| 7 | 7N1P|1|5 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ELECTRON MICROSCOPY | 2.33 | 120 |
| 8 | 8AKN|1|b | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | ELECTRON MICROSCOPY | 2.3 | 119 |
| 9 | 8ANA|1|b | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit | ELECTRON MICROSCOPY | 2.1 | 119 |
| 10 | 8EMM|1|b | Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates | ELECTRON MICROSCOPY | 2.1 | 119 |
| 11 | 8G6X|1|b | Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site meta-aminobenzoic acid charged NH-tRNAPhe | ELECTRON MICROSCOPY | 2.31 | 119 |
| 12 | 8EIU|1|b | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | ELECTRON MICROSCOPY | 2.24 | 119 |
| 13 | 7K00|1|b | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | ELECTRON MICROSCOPY | 1.98 | 119 |
| 14 | 8AYE|1|b | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ELECTRON MICROSCOPY | 1.96 | 119 |
| 15 | 8G6Y|1|b | Structure of WT E.coli ribosome 50S subunit with complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site 3-aminopyridine-4-carboxylic acid charged NH-tRNAPhe | ELECTRON MICROSCOPY | 2.09 | 119 |
| 16 | 8G6W|1|b | Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe | ELECTRON MICROSCOPY | 2.02 | 119 |
| 17 | 8B0X|1|b | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | ELECTRON MICROSCOPY | 1.55 | 119 |
| 18 | 7O1A|1|BB | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | ELECTRON MICROSCOPY | 2.4 | 120 |
| 19 | 7QQ3|1|J | Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. | ELECTRON MICROSCOPY | 2.1 | 118 |
| 20 | 7S1I|1|J | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.48 | 118 |
| 21 | 7S1G|1|J | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.48 | 118 |
| 22 | 7S1H|1|J | Wild-type Escherichia coli ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.35 | 118 |
| 23 | 7S1K|1|J | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.42 | 118 |
| 24 | 7S1J|1|J | Wild-type Escherichia coli ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.47 | 118 |
| 25 | 6PCR|1|J | E. coli 50S ribosome bound to compound 40o | ELECTRON MICROSCOPY | 2.5 | 118 |
| 26 | 6PC6|1|J | E. coli 50S ribosome bound to compound 47 | ELECTRON MICROSCOPY | 2.5 | 118 |
| 27 | 6PC7|1|J | E. coli 50S ribosome bound to compound 46 | ELECTRON MICROSCOPY | 2.5 | 118 |
| 28 | 7BL4|1|B | in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle | ELECTRON MICROSCOPY | 2.4 | 119 |
| 29 | 7Z20|1|a | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | ELECTRON MICROSCOPY | 2.29 | 118 |
| 30 | 7ZP8|1|a | 70S E. coli ribosome with a stalled filamin domain 5 nascent chain | ELECTRON MICROSCOPY | 2.2 | 118 |