Equivalence class NR_2.5_83717.105 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4YBB|1|DA (rep) | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2897 | 2015-03-18 |
| 2 | 4YBB|1|CA | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2898 | 2015-03-18 |
| 3 | 8B0X|1|a | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli B | Bacteria | RF02541 | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | Electron microscopy | 1.55 | 2748 | 2022-11-30 |
| 4 | 7ZP8|1|b | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | 70S E. coli ribosome with a stalled filamin domain 5 nascent chain | Electron microscopy | 2.2 | 2901 | 2022-08-10 |
| 5 | 7K00|1|a | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | Electron microscopy | 1.98 | 2753 | 2020-09-23 |
| 6 | 6XZ7|1|A | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | Electron microscopy | 2.1 | 2897 | 2020-07-22 |
| 7 | 7Z20|1|b | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | Electron microscopy | 2.29 | 2901 | 2022-08-10 |
| 8 | 7LVK|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Cfr-modified 50S subunit from Escherichia coli | Electron microscopy | 2.2 | 2898 | 2021-12-15 |
| 9 | 6PJ6|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | High resolution cryo-EM structure of E.coli 50S | Electron microscopy | 2.2 | 2898 | 2020-01-22 |
| 10 | 7N1P|1|23 | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli K-12 | Bacteria | RF02541 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | Electron microscopy | 2.33 | 2904 | 2021-07-14 |
| 11 | 7PJS|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Escherichia coli | Bacteria | RF02541 | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | Electron microscopy | 2.35 | 2903 | 2021-10-20 |
| 12 | 7S1H|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Wild-type Escherichia coli ribosome with antibiotic linezolid | Electron microscopy | 2.35 | 2898 | 2021-11-17 |
| 13 | 7S1K|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.42 | 2898 | 2022-01-19 |
| 14 | 7O1A|1|BA | Large subunit ribosomal RNA | Ribosomal RNA 23S | Escherichia coli K-12 | Bacteria | RF02541 | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | Electron microscopy | 2.4 | 2897 | 2021-09-01 |
| 15 | 7S1J|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Wild-type Escherichia coli ribosome with antibiotic radezolid | Electron microscopy | 2.47 | 2898 | 2022-03-02 |
| 16 | 7S1I|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.48 | 2898 | 2022-03-02 |
| 17 | 7S1G|1|I | Large subunit ribosomal RNA | 23S rRNA | Escherichia coli | Bacteria | RF02541 | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | Electron microscopy | 2.48 | 2898 | 2021-11-17 |
| 18 | 7BL4|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Escherichia coli K-12 | Bacteria | RF02541 | in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle | Electron microscopy | 2.4 | 2897 | 2021-05-12 |
| 19 | 6PCR|1|I | Large subunit ribosomal RNA | 23S ribosomal RNA | Escherichia coli | Bacteria | RF02541 | E. coli 50S ribosome bound to compound 40o | Electron microscopy | 2.5 | 2897 | 2020-06-17 |
| 20 | 6PC6|1|I | Large subunit ribosomal RNA | 23S ribosomal RNA | Escherichia coli | Bacteria | RF02541 | E. coli 50S ribosome bound to compound 47 | Electron microscopy | 2.5 | 2897 | 2020-06-17 |
| 21 | 6PC7|1|I | Large subunit ribosomal RNA | 23S ribosomal RNA | Escherichia coli | Bacteria | RF02541 | E. coli 50S ribosome bound to compound 46 | Electron microscopy | 2.5 | 2897 | 2020-06-17 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_83717.105 | NR_2.5_83717.104 | 3.264 | (21) 4YBB|1|CA, 4YBB|1|DA, 6PC6|1|I, 6PC7|1|I, 6PCR|1|I, 6PJ6|1|I, 6XZ7|1|A, 7BL4|1|A, 7K00|1|a, 7LVK|1|I, 7N1P|1|23, 7O1A|1|BA, 7PJS|1|A, 7S1G|1|I, 7S1H|1|I, 7S1I|1|I, 7S1J|1|I, 7S1K|1|I, 7Z20|1|b, 7ZP8|1|b, 8B0X|1|a | (0) | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_83717.105 | NR_2.5_83717.106 | 3.266 | (21) 4YBB|1|CA, 4YBB|1|DA, 6PC6|1|I, 6PC7|1|I, 6PCR|1|I, 6PJ6|1|I, 6XZ7|1|A, 7BL4|1|A, 7K00|1|a, 7LVK|1|I, 7N1P|1|23, 7O1A|1|BA, 7PJS|1|A, 7S1G|1|I, 7S1H|1|I, 7S1I|1|I, 7S1J|1|I, 7S1K|1|I, 7Z20|1|b, 7ZP8|1|b, 8B0X|1|a | (0) | (1) 7QQ3|1|I |
Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.
| #S | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 1 | 4YBB|1|DA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 2897 | |
| 2 | 6XZ7|1|A | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | ELECTRON MICROSCOPY | 2.1 | 2897 | |
| 3 | 7K00|1|a | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | ELECTRON MICROSCOPY | 1.98 | 2753 | |
| 4 | 7N1P|1|23 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ELECTRON MICROSCOPY | 2.33 | 2904 | |
| 5 | 7S1J|1|I | Wild-type Escherichia coli ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.47 | 2898 | |
| 6 | 7S1I|1|I | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.48 | 2898 | |
| 7 | 7S1G|1|I | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.48 | 2898 | |
| 8 | 7S1H|1|I | Wild-type Escherichia coli ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.35 | 2898 | |
| 9 | 7S1K|1|I | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.42 | 2898 | |
| 10 | 8B0X|1|a | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | ELECTRON MICROSCOPY | 1.55 | 2748 | |
| 11 | 7Z20|1|b | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | ELECTRON MICROSCOPY | 2.29 | 2901 | |
| 12 | 7ZP8|1|b | 70S E. coli ribosome with a stalled filamin domain 5 nascent chain | ELECTRON MICROSCOPY | 2.2 | 2901 | |
| 13 | 7O1A|1|BA | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | ELECTRON MICROSCOPY | 2.4 | 2897 | |
| 14 | 7PJS|1|A | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | ELECTRON MICROSCOPY | 2.35 | 2903 | |
| 15 | 7BL4|1|A | in vitro reconstituted 50S-ObgE-GMPPNP-RsfS particle | ELECTRON MICROSCOPY | 2.4 | 2897 | |
| 16 | 6PC6|1|I | E. coli 50S ribosome bound to compound 47 | ELECTRON MICROSCOPY | 2.5 | 2897 | |
| 17 | 6PCR|1|I | E. coli 50S ribosome bound to compound 40o | ELECTRON MICROSCOPY | 2.5 | 2897 | |
| 18 | 6PC7|1|I | E. coli 50S ribosome bound to compound 46 | ELECTRON MICROSCOPY | 2.5 | 2897 | |
| 19 | 6PJ6|1|I | High resolution cryo-EM structure of E.coli 50S | ELECTRON MICROSCOPY | 2.2 | 2898 | |
| 20 | 7LVK|1|I | Cfr-modified 50S subunit from Escherichia coli | ELECTRON MICROSCOPY | 2.2 | 2898 | |
| 21 | 4YBB|1|CA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 2898 |
Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.
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