Equivalence class NR_20.0_53472.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 4DR7|1|b (rep) | 5'-R(P*UP*UP*U)-3' | Thermus thermophilus | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound | X-ray diffraction | 3.75 | 3 | 2012-11-14 | |||
| 2 | 1I5L|1|Y | 5'-R(*UP*UP*U)-3' | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA | X-ray diffraction | 2.75 | 3 | 2001-08-28 | ||||
| 3 | 1I5L|1|U | 5'-R(*UP*UP*U)-3' | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA | X-ray diffraction | 2.75 | 3 | 2001-08-28 | ||||
| 4 | 4DR6|1|b | 5'-R(*UP*UP*U)-3' | Thermus thermophilus | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound | X-ray diffraction | 3.3 | 2 | 2012-11-14 | |||
| 5 | 8V9J|1|v | poly-U mRNA | Mycolicibacterium smegmatis MC2 155 | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) (Structure 4) | Electron microscopy | 3.1 | 3 | 2024-02-07 | |||
| 6 | 8V9K|1|v | poly-U mRNA | Mycolicibacterium smegmatis MC2 155 | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Rv2629 (Balon) (Structure 5) | Electron microscopy | 3.1 | 3 | 2024-02-07 | |||
| 7 | 6I2N|1|U | RNA (5'-R(P*UP*UP*U)-3') | Spodoptera frugiperda | Helical RNA-bound Hantaan virus nucleocapsid | Electron microscopy | 3.3 | 3 | 2019-01-23 | |||
| 8 | 4V68|1|A0 | MRNA CODON | T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. | Electron microscopy | 6.4 | 3 | 2014-07-09 | ||||
| 9 | 6VYU|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C2 (TTC-C2) containing a 27 nt long mRNA spacer | Electron microscopy | 7 | 3 | 2020-09-02 | |||
| 10 | 6VYW|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C3 (TTC-C3) containing mRNA with a 27 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | Electron microscopy | 7 | 3 | 2020-09-02 | |||
| 11 | 6VZ7|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C1 (TTC-C1) containing a 27 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site | Electron microscopy | 7 | 3 | 2020-09-02 | |||
| 12 | 6VZ5|1|Y | mRNA in the ribosomal RNA entrance pore | Escherichia coli | Escherichia coli transcription-translation complex D3 (TTC-D3) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | Electron microscopy | 8.9 | 3 | 2020-09-02 | |||
| 13 | 6VZ3|1|Y | mRNA in the ribosomal RNA entrance pore | Escherichia coli | Escherichia coli transcription-translation complex D2 (TTC-D2) containing mRNA with a 27 nt long spacer | Electron microscopy | 8.9 | 3 | 2020-09-02 | |||
| 14 | 6VYY|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C5 (TTC-C5) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | Electron microscopy | 9.9 | 3 | 2020-09-02 | |||
| 15 | 6VYX|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C4 (TTC-C4) containing mRNA with a 21 nt long spacer, transcription factor NusG, and fMet-tRNAs at P-site and E-site | Electron microscopy | 9.9 | 3 | 2020-09-02 | |||
| 16 | 6VYZ|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex C6 (TTC-C6) containing mRNA with a 21 nt long spacer, NusA, and fMet-tRNAs at E-site and P-site | Electron microscopy | 9.9 | 3 | 2020-09-02 | |||
| 17 | 6VZ2|1|Y | mRNA in the ribosomal RNA entrance pore | Escherichia coli | Escherichia coli transcription-translation complex D1 (TTC-D1) containing mRNA with a 27 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | Electron microscopy | 10 | 3 | 2020-09-02 | |||
| 18 | 1MVR|1|1 | mRNA, triplet codon (A-site) | Escherichia coli | Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome | Electron microscopy | 12.8 | 3 | 2003-04-01 | |||
| 19 | 6VYT|1|Y | mRNA in the ribosomal RNA entrance pore | synthetic construct | Escherichia coli transcription-translation complex A2 (TTC-A2) containing a 15 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site | Electron microscopy | 14 | 3 | 2020-09-02 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | 1MVR|1|1 | Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome | ELECTRON MICROSCOPY | 12.8 | 3 | |
| 2 | 6VYX|1|Y | Escherichia coli transcription-translation complex C4 (TTC-C4) containing mRNA with a 21 nt long spacer, transcription factor NusG, and fMet-tRNAs at P-site and E-site | ELECTRON MICROSCOPY | 9.9 | 3 | |
| 3 | 6VZ3|1|Y | Escherichia coli transcription-translation complex D2 (TTC-D2) containing mRNA with a 27 nt long spacer | ELECTRON MICROSCOPY | 8.9 | 3 | |
| 4 | 6VYW|1|Y | Escherichia coli transcription-translation complex C3 (TTC-C3) containing mRNA with a 27 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | ELECTRON MICROSCOPY | 7 | 3 | |
| 5 | 6VZ7|1|Y | Escherichia coli transcription-translation complex C1 (TTC-C1) containing a 27 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site | ELECTRON MICROSCOPY | 7 | 3 | |
| 6 | 6VYU|1|Y | Escherichia coli transcription-translation complex C2 (TTC-C2) containing a 27 nt long mRNA spacer | ELECTRON MICROSCOPY | 7 | 3 | |
| 7 | 6VYZ|1|Y | Escherichia coli transcription-translation complex C6 (TTC-C6) containing mRNA with a 21 nt long spacer, NusA, and fMet-tRNAs at E-site and P-site | ELECTRON MICROSCOPY | 9.9 | 3 | |
| 8 | 6VYY|1|Y | Escherichia coli transcription-translation complex C5 (TTC-C5) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | ELECTRON MICROSCOPY | 9.9 | 3 | |
| 9 | 6VYT|1|Y | Escherichia coli transcription-translation complex A2 (TTC-A2) containing a 15 nt long mRNA spacer, NusG, and fMet-tRNAs at P-site and E-site | ELECTRON MICROSCOPY | 14 | 3 | |
| 10 | 6VZ5|1|Y | Escherichia coli transcription-translation complex D3 (TTC-D3) containing mRNA with a 21 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | ELECTRON MICROSCOPY | 8.9 | 3 | |
| 11 | 1I5L|1|Y | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA | X-RAY DIFFRACTION | 2.75 | 3 | |
| 12 | 1I5L|1|U | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA | X-RAY DIFFRACTION | 2.75 | 3 | |
| 13 | 6VZ2|1|Y | Escherichia coli transcription-translation complex D1 (TTC-D1) containing mRNA with a 27 nt long spacer, NusG, and fMet-tRNAs at E-site and P-site | ELECTRON MICROSCOPY | 10 | 3 | |
| 14 | 8V9J|1|v | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) (Structure 4) | ELECTRON MICROSCOPY | 3.1 | 3 | |
| 15 | 8V9K|1|v | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Rv2629 (Balon) (Structure 5) | ELECTRON MICROSCOPY | 3.1 | 3 | |
| 16 | 4V68|1|A0 | T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map. | ELECTRON MICROSCOPY | 6.4 | 3 | |
| 17 | 6I2N|1|U | Helical RNA-bound Hantaan virus nucleocapsid | ELECTRON MICROSCOPY | 3.3 | 3 | |
| 18 | 4DR7|1|b | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound | X-RAY DIFFRACTION | 3.75 | 3 | |
| 19 | 4DR6|1|b | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound | X-RAY DIFFRACTION | 3.3 | 2 |
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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