Equivalence class NR_2.5_56726.103 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4YBB|1|AA (rep) | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2015-03-18 |
| 2 | 4YBB|1|BA | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 2015-03-18 |
| 3 | 8B0X|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli B | Bacteria | RF00177 | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | Electron microscopy | 1.55 | 2022-11-30 |
| 4 | 8AYE|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | Electron microscopy | 1.96 | 2023-03-01 |
| 5 | 7K00|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | Electron microscopy | 1.98 | 2020-09-23 |
| 6 | 8G6W|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | 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 | 8EMM|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | 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 |
| 8 | 8EIU|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | Electron microscopy | 2.24 | 2023-02-01 |
| 9 | 7S1H|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli ribosome with antibiotic linezolid | Electron microscopy | 2.35 | 2021-11-17 |
| 10 | 7N1P|1|16 | Small subunit ribosomal RNA | 16S rRNA, mRNA | Escherichia coli K-12 | Bacteria | RF00177 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | Electron microscopy | 2.33 | 2021-07-14 |
| 11 | 8AKN|1|B | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00177 | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | Electron microscopy | 2.3 | 2023-03-08 |
| 12 | 7S1K|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.42 | 2022-01-19 |
| 13 | 7S1J|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli ribosome with antibiotic radezolid | Electron microscopy | 2.47 | 2022-03-02 |
| 14 | 7S1I|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.48 | 2022-03-02 |
| 15 | 7S1G|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | Electron microscopy | 2.48 | 2021-11-17 |
| 16 | 7O1A|1|AA | Small subunit ribosomal RNA | Ribosomal RNA 16S | Escherichia coli K-12 | Bacteria | RF00177 | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | Electron microscopy | 2.4 | 2021-09-01 |
| 17 | 8CGJ|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Streptomycin bound to the 30S body | Electron microscopy | 1.79 | 2023-07-26 |
| 18 | 8CGU|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Gentamicin bound to the 30S body | Electron microscopy | 1.89 | 2023-07-26 |
| 19 | 8CAI|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Streptomycin and Hygromycin B bound to the 30S body | Electron microscopy | 2.08 | 2023-07-26 |
| 20 | 8CEP|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Round2 30S head (no antibiotic) | Electron microscopy | 2.04 | 2023-07-19 |
| 21 | 8CGR|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Apramycin bound to the 30S body | Electron microscopy | 2.12 | 2023-07-26 |
| 22 | 8CF1|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Tetracycline bound to the 30S head | Electron microscopy | 1.82 | 2023-07-26 |
| 23 | 7PJS|1|a | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli | Bacteria | RF00177 | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | Electron microscopy | 2.35 | 2021-10-20 |
| 24 | 8CGI|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Pentacycline TP038 bound to the 30S head | Electron microscopy | 1.89 | 2023-07-26 |
| 25 | 8CAZ|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | empty 30S head | Electron microscopy | 2.11 | 2023-07-26 |
Release history
| Release | 3.293 |
|---|---|
| Date | 2023-07-26 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_2.5_56726.103 | NR_2.5_56726.102 | 3.293 | (18) 4YBB|1|AA, 4YBB|1|BA, 7K00|1|A, 7N1P|1|16, 7O1A|1|AA, 7PJS|1|a, 7S1G|1|C, 7S1H|1|C, 7S1I|1|C, 7S1J|1|C, 7S1K|1|C, 8AKN|1|B, 8AYE|1|A, 8B0X|1|A, 8CEP|1|A, 8EIU|1|A, 8EMM|1|A, 8G6W|1|A | (7) 8CAI|1|A, 8CAZ|1|A, 8CF1|1|A, 8CGI|1|A, 8CGJ|1|A, 8CGR|1|A, 8CGU|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_2.5_56726.103 | NR_2.5_56726.104 | 3.294 | (25) 4YBB|1|AA, 4YBB|1|BA, 7K00|1|A, 7N1P|1|16, 7O1A|1|AA, 7PJS|1|a, 7S1G|1|C, 7S1H|1|C, 7S1I|1|C, 7S1J|1|C, 7S1K|1|C, 8AKN|1|B, 8AYE|1|A, 8B0X|1|A, 8CAI|1|A, 8CAZ|1|A, 8CEP|1|A, 8CF1|1|A, 8CGI|1|A, 8CGJ|1|A, 8CGR|1|A, 8CGU|1|A, 8EIU|1|A, 8EMM|1|A, 8G6W|1|A | (0) | (3) 8CA7|1|A, 8CF8|1|A, 8FTO|1|A |
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 | Length |
|---|---|---|---|---|---|---|
| 1 | 8CAZ|1|A | empty 30S head | ELECTRON MICROSCOPY | 2.11 | 457 | |
| 2 | 8CGI|1|A | Pentacycline TP038 bound to the 30S head | ELECTRON MICROSCOPY | 1.89 | 457 | |
| 3 | 8CF1|1|A | Tetracycline bound to the 30S head | ELECTRON MICROSCOPY | 1.82 | 481 | |
| 4 | 8CGJ|1|A | Streptomycin bound to the 30S body | ELECTRON MICROSCOPY | 1.79 | 1122 | |
| 5 | 8EIU|1|A | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | ELECTRON MICROSCOPY | 2.24 | 1508 | |
| 6 | 7K00|1|A | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | ELECTRON MICROSCOPY | 1.98 | 1508 | |
| 7 | 8EMM|1|A | Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates | ELECTRON MICROSCOPY | 2.1 | 1508 | |
| 8 | 8G6W|1|A | 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 | 1508 | |
| 9 | 7N1P|1|16 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ELECTRON MICROSCOPY | 2.33 | 1531 | |
| 10 | 8CAI|1|A | Streptomycin and Hygromycin B bound to the 30S body | ELECTRON MICROSCOPY | 2.08 | 1105 | |
| 11 | 8AKN|1|B | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | ELECTRON MICROSCOPY | 2.3 | 1510 | |
| 12 | 8AYE|1|A | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ELECTRON MICROSCOPY | 1.96 | 1508 | |
| 13 | 7S1H|1|C | Wild-type Escherichia coli ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.35 | 1540 | |
| 14 | 7S1G|1|C | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.48 | 1540 | |
| 15 | 7S1I|1|C | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.48 | 1540 | |
| 16 | 7S1K|1|C | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.42 | 1540 | |
| 17 | 7S1J|1|C | Wild-type Escherichia coli ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.47 | 1540 | |
| 18 | 8B0X|1|A | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | ELECTRON MICROSCOPY | 1.55 | 1489 | |
| 19 | 7O1A|1|AA | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | ELECTRON MICROSCOPY | 2.4 | 1523 | |
| 20 | 8CGU|1|A | Gentamicin bound to the 30S body | ELECTRON MICROSCOPY | 1.89 | 1039 | |
| 21 | 8CGR|1|A | Apramycin bound to the 30S body | ELECTRON MICROSCOPY | 2.12 | 1052 | |
| 22 | 8CEP|1|A | Round2 30S head (no antibiotic) | ELECTRON MICROSCOPY | 2.04 | 1038 | |
| 23 | 4YBB|1|BA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 1522 | |
| 24 | 4YBB|1|AA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 1523 | |
| 25 | 7PJS|1|a | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | ELECTRON MICROSCOPY | 2.35 | 660 |
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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