Equivalence class NR_20.0_92489.4 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 8RZA|1|R (rep) | RNA (5'-R(P*UP*UP*U)-3') | Escherichia coli | Ribonuclease W | X-ray diffraction | 2.1 | 3 | 2024-11-06 | |||
| 2 | 4DR7|1|b | 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 | |||
| 3 | 4DR5|1|V | 5'-R(*UP*UP*U)-3' | Thermus thermophilus | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered cognate transfer RNA anticodon stem-loop and streptomycin bound | X-ray diffraction | 3.45 | 3 | 2012-11-14 | |||
| 4 | 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 | ||||
| 5 | 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 | ||||
| 6 | 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 | |||
| 7 | 5IP2|1|D | RNA (5'-D(P*UP*UP*U)-3') | synthetic construct | Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex | X-ray diffraction | 3.3 | 3 | 2017-03-22 | |||
| 8 | 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 | |||
| 9 | 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 | |||
| 10 | 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 | ||||
| 11 | 486D|1|B | P-SITE CODON OF 70S RIBOSOME | X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES | X-ray diffraction | 7.5 | 3 | 1999-10-04 | ||||
| 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 | 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 | |||
| 14 | 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 |
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 | 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 | |
| 2 | 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 | |
| 3 | 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 | |
| 4 | 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 | |
| 5 | 6I2N|1|U | Helical RNA-bound Hantaan virus nucleocapsid | ELECTRON MICROSCOPY | 3.3 | 3 | |
| 6 | 5IP2|1|D | Tomato spotted wilt tospovirus nucleocapsid protein-ssRNA complex | X-RAY DIFFRACTION | 3.3 | 3 | |
| 7 | 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 | |
| 8 | 4DR5|1|V | Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered cognate transfer RNA anticodon stem-loop and streptomycin bound | X-RAY DIFFRACTION | 3.45 | 3 | |
| 9 | 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 | |
| 10 | 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 | |
| 11 | 486D|1|B | X-RAY CRYSTAL STRUCTURES OF 70S RIBOSOME FUNCTIONAL COMPLEXES | X-RAY DIFFRACTION | 7.5 | 3 | |
| 12 | 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 | |
| 13 | 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 | |
| 14 | 8RZA|1|R | Ribonuclease W | X-RAY DIFFRACTION | 2.1 | 3 |
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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