Equivalence class NR_3.0_18586.53 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5TBW|1|AS (rep) | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2017-07-26 |
| 2 | 5TBW|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2017-07-26 |
| 3 | 4V88|1|A3 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | The structure of the eukaryotic ribosome at 3.0 A resolution. | X-ray diffraction | 3 | 2014-07-09 |
| 4 | 4V88|1|A7 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | The structure of the eukaryotic ribosome at 3.0 A resolution. | X-ray diffraction | 3 | 2014-07-09 |
| 5 | 7OSA|1|AB | 5S ribosomal RNA | 5S | Saccharomyces cerevisiae | Eukarya | RF00001 | Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands | X-ray diffraction | 3 | 2021-12-08 |
| 6 | 7OSM|1|AB | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands | X-ray diffraction | 3 | 2021-12-08 |
| 7 | 7ZW0|1|LC | 5S ribosomal RNA | 5S ribosomal RNA (RDN5-1) | Saccharomyces cerevisiae W303 | Eukarya | RF00001 | FAP-80S Complex - Rotated state | Electron microscopy | 2.4 | 2022-10-05 |
| 8 | 8AGX|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state with the RING domain of Ltn1 in the IN position | Electron microscopy | 2.4 | 2023-03-08 |
| 9 | 7TOP|1|A5S | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 | Electron microscopy | 2.4 | 2022-05-25 |
| 10 | 7ZUX|1|4 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Collided ribosome in a disome unit from S. cerevisiae | Electron microscopy | 2.5 | 2023-02-22 |
| 11 | 8AAF|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state G | Electron microscopy | 2.5 | 2023-03-08 |
| 12 | 6T4Q|1|C4 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. | Electron microscopy | 2.6 | 2019-12-25 |
| 13 | 8AGW|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state D | Electron microscopy | 2.6 | 2023-03-08 |
| 14 | 8AGT|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state F | Electron microscopy | 2.6 | 2023-03-08 |
| 15 | 8AGV|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state H | Electron microscopy | 2.6 | 2023-03-08 |
| 16 | 8AGZ|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position | Electron microscopy | 2.6 | 2023-03-08 |
| 17 | 8AGU|1|h | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast RQC complex in state E | Electron microscopy | 2.7 | 2023-03-08 |
| 18 | 7TOO|1|A5S | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 | Electron microscopy | 2.7 | 2022-05-25 |
| 19 | 7MPJ|1|A3 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Stm1 bound vacant 80S structure isolated from nop1-D243A | Electron microscopy | 2.7 | 2022-05-11 |
| 20 | 6TB3|1|BR | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex | Electron microscopy | 2.8 | 2020-04-22 |
| 21 | 6SNT|1|4 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Yeast 80S ribosome stalled on SDD1 mRNA. | Electron microscopy | 2.8 | 2020-03-04 |
| 22 | 7AZY|1|F | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae S288C | Eukarya | RF00001 | Context-specific inhibition of eukaryotic translation by macrolide antibiotics | Electron microscopy | 2.877 | 2021-05-19 |
| 23 | 4U4R|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Lactimidomycin bound to the yeast 80S ribosome | X-ray diffraction | 2.8 | 2014-10-22 |
| 24 | 4U3U|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Cycloheximide bound to the yeast 80S ribosome | X-ray diffraction | 2.9 | 2014-10-22 |
| 25 | 6WOO|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP | Electron microscopy | 2.9 | 2020-09-23 |
| 26 | 7UG6|1|3 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae S288C | Eukarya | RF00001 | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 | Electron microscopy | 2.9 | 2022-12-21 |
| 27 | 4U4R|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Lactimidomycin bound to the yeast 80S ribosome | X-ray diffraction | 2.8 | 2014-10-22 |
| 28 | 4U3U|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Cycloheximide bound to the yeast 80S ribosome | X-ray diffraction | 2.9 | 2014-10-22 |
| 29 | 4U4Q|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Homoharringtonine bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 30 | 4U4Q|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Homoharringtonine bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 31 | 4U3M|1|7 | 5S ribosomal RNA | 5.8s rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Anisomycin bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 32 | 4U52|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Nagilactone C bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 33 | 4U3M|1|3 | 5S ribosomal RNA | 5.8s rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Anisomycin bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 34 | 4U4U|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Lycorine bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 35 | 6YLG|1|3 | 5S ribosomal RNA | 5S rRNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) | Electron microscopy | 3 | 2020-07-29 |
| 36 | 4U52|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Nagilactone C bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
| 37 | 4U4U|1|3 | 5S ribosomal RNA | 5S ribosomal RNA | Saccharomyces cerevisiae | Eukarya | RF00001 | Crystal structure of Lycorine bound to the yeast 80S ribosome | X-ray diffraction | 3 | 2014-10-22 |
Release history
| Release | 3.273 |
|---|---|
| Date | 2023-03-08 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.0_18586.53 | NR_3.0_18586.52 | 3.273 | (30) 4U4R|1|7, 7AZY|1|F, 4V88|1|A3, 7TOP|1|A5S, 4U3U|1|7, 6SNT|1|4, 4U3U|1|3, 4U52|1|7, 7TOO|1|A5S, 6YLG|1|3, 4U4R|1|3, 5TBW|1|AS, 7ZW0|1|LC, 4U3M|1|7, 4U52|1|3, 7OSM|1|AB, 6WOO|1|7, 4U4Q|1|7, 5TBW|1|3, 7ZUX|1|4, 7OSA|1|AB, 4U3M|1|3, 4U4U|1|7, 6TB3|1|BR, 4U4Q|1|3, 4V88|1|A7, 7UG6|1|3, 7MPJ|1|A3, 4U4U|1|3, 6T4Q|1|C4 | (7) 8AGX|1|h, 8AGV|1|h, 8AGU|1|h, 8AGT|1|h, 8AGZ|1|h, 8AGW|1|h, 8AAF|1|h | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.0_18586.53 | NR_3.0_18586.54 | 3.274 | (37) 4U4Q|1|7, 7ZW0|1|LC, 4U4U|1|7, 8AGV|1|h, 4V88|1|A7, 6T4Q|1|C4, 7AZY|1|F, 4U3M|1|7, 7TOO|1|A5S, 7ZUX|1|4, 4U4U|1|3, 8AGU|1|h, 4V88|1|A3, 8AGZ|1|h, 6SNT|1|4, 6YLG|1|3, 4U3M|1|3, 7OSM|1|AB, 4U4Q|1|3, 7UG6|1|3, 4U4R|1|7, 8AGT|1|h, 4U52|1|7, 8AGX|1|h, 5TBW|1|AS, 6WOO|1|7, 7OSA|1|AB, 4U3U|1|7, 7TOP|1|A5S, 4U4R|1|3, 8AAF|1|h, 4U52|1|3, 8AGW|1|h, 5TBW|1|3, 6TB3|1|BR, 7MPJ|1|A3, 4U3U|1|3 | (0) | (4) 7UQB|1|3, 7UOO|1|3, 7V08|1|3, 7UQZ|1|3 |
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 | 6YLG|1|3 | Rix1-Rea1 pre-60S particle - 60S core, body 1 (rigid body refinement) | ELECTRON MICROSCOPY | 3 | 117 |
| 2 | 7ZUX|1|4 | Collided ribosome in a disome unit from S. cerevisiae | ELECTRON MICROSCOPY | 2.5 | 121 |
| 3 | 7ZW0|1|LC | FAP-80S Complex - Rotated state | ELECTRON MICROSCOPY | 2.4 | 121 |
| 4 | 8AGW|1|h | Yeast RQC complex in state D | ELECTRON MICROSCOPY | 2.6 | 121 |
| 5 | 8AGU|1|h | Yeast RQC complex in state E | ELECTRON MICROSCOPY | 2.7 | 121 |
| 6 | 8AGV|1|h | Yeast RQC complex in state H | ELECTRON MICROSCOPY | 2.6 | 121 |
| 7 | 8AGT|1|h | Yeast RQC complex in state F | ELECTRON MICROSCOPY | 2.6 | 121 |
| 8 | 8AGX|1|h | Yeast RQC complex in state with the RING domain of Ltn1 in the IN position | ELECTRON MICROSCOPY | 2.4 | 121 |
| 9 | 8AAF|1|h | Yeast RQC complex in state G | ELECTRON MICROSCOPY | 2.5 | 121 |
| 10 | 8AGZ|1|h | Yeast RQC complex in state with the RING domain of Ltn1 in the OUT position | ELECTRON MICROSCOPY | 2.6 | 121 |
| 11 | 6TB3|1|BR | yeast 80S ribosome in complex with the Not5 subunit of the CCR4-NOT complex | ELECTRON MICROSCOPY | 2.8 | 121 |
| 12 | 6SNT|1|4 | Yeast 80S ribosome stalled on SDD1 mRNA. | ELECTRON MICROSCOPY | 2.8 | 121 |
| 13 | 6T4Q|1|C4 | Structure of yeast 80S ribosome stalled on the CGA-CCG inhibitory codon combination. | ELECTRON MICROSCOPY | 2.6 | 121 |
| 14 | 7TOP|1|A5S | Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 | ELECTRON MICROSCOPY | 2.4 | 121 |
| 15 | 7TOO|1|A5S | Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 | ELECTRON MICROSCOPY | 2.7 | 121 |
| 16 | 5TBW|1|3 | Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 17 | 4V88|1|A3 | The structure of the eukaryotic ribosome at 3.0 A resolution. | X-RAY DIFFRACTION | 3 | 121 |
| 18 | 4U4R|1|3 | Crystal structure of Lactimidomycin bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 2.8 | 121 |
| 19 | 4U3U|1|3 | Crystal structure of Cycloheximide bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 2.9 | 121 |
| 20 | 4U3M|1|3 | Crystal structure of Anisomycin bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 21 | 4U4U|1|3 | Crystal structure of Lycorine bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 22 | 4U4Q|1|3 | Crystal structure of Homoharringtonine bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 23 | 4U52|1|3 | Crystal structure of Nagilactone C bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 24 | 5TBW|1|AS | Crystal structure of chlorolissoclimide bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 25 | 4U52|1|7 | Crystal structure of Nagilactone C bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 26 | 4U4U|1|7 | Crystal structure of Lycorine bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 27 | 4U4Q|1|7 | Crystal structure of Homoharringtonine bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 28 | 4U3M|1|7 | Crystal structure of Anisomycin bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 3 | 121 |
| 29 | 4U4R|1|7 | Crystal structure of Lactimidomycin bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 2.8 | 121 |
| 30 | 4U3U|1|7 | Crystal structure of Cycloheximide bound to the yeast 80S ribosome | X-RAY DIFFRACTION | 2.9 | 121 |
| 31 | 4V88|1|A7 | The structure of the eukaryotic ribosome at 3.0 A resolution. | X-RAY DIFFRACTION | 3 | 121 |
| 32 | 6WOO|1|7 | CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP | ELECTRON MICROSCOPY | 2.9 | 121 |
| 33 | 7MPJ|1|A3 | Stm1 bound vacant 80S structure isolated from nop1-D243A | ELECTRON MICROSCOPY | 2.7 | 120 |
| 34 | 7AZY|1|F | Context-specific inhibition of eukaryotic translation by macrolide antibiotics | ELECTRON MICROSCOPY | 2.877 | 121 |
| 35 | 7OSA|1|AB | Pre-translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands | X-RAY DIFFRACTION | 3 | 121 |
| 36 | 7OSM|1|AB | Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligands | X-RAY DIFFRACTION | 3 | 121 |
| 37 | 7UG6|1|3 | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 | ELECTRON MICROSCOPY | 2.9 | 121 |