Equivalence class NR_all_41610.15 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 6TPQ|1|U (rep) | Large subunit ribosomal RNA | pre-23S rRNA | Bacillus subtilis | Bacteria | RF02541 | RNase M5 bound to 50S ribosome with precursor 5S rRNA | Electron microscopy | 3.07 | 2020-09-30 |
| 2 | 7AQD|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Structure of the bacterial RQC complex (Translocating State) | Electron microscopy | 3.1 | 2020-11-25 |
| 3 | 7AQC|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Structure of the bacterial RQC complex (Decoding State) | Electron microscopy | 2.99 | 2020-11-25 |
| 4 | 6TNN|1|U | Large subunit ribosomal RNA | pre-23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA | Electron microscopy | 3.07 | 2020-09-30 |
| 5 | 7AS8|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | Electron microscopy | 2.9 | 2020-12-09 |
| 6 | 6HA1|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis | Bacteria | RF02541 | Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycin | Electron microscopy | 3.1 | 2018-08-29 |
| 7 | 7O5B|1|X | Large subunit ribosomal RNA | 23S rRNA (2887-MER) | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound | Electron microscopy | 3.33 | 2022-02-02 |
| 8 | 7OPE|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement) | Electron microscopy | 3.2 | 2021-07-21 |
| 9 | 7QV1|1|V | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis collided disome (Leading 70S) | Electron microscopy | 3.5 | 2022-03-09 |
| 10 | 7QV2|1|V | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis collided disome (Collided 70S) | Electron microscopy | 3.5 | 2022-03-09 |
| 11 | 7AS9|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH. | Electron microscopy | 3.5 | 2020-12-23 |
| 12 | 6HA8|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome | Electron microscopy | 3.5 | 2018-08-29 |
| 13 | 7SAE|1|A | Large subunit ribosomal RNA | RNA (2434-MER) | Bacillus subtilis | Bacteria | RF02541 | 44SR70P Class1 ribosomal particle | Electron microscopy | 3 | 2022-03-02 |
| 14 | 5NJT|1|U | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis | Bacteria | RF02541 | Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. | Electron microscopy | 3.8 | 2017-06-14 |
| 15 | 3J9W|1|BA | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis | Bacteria | RF02541 | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | Electron microscopy | 3.9 | 2015-04-29 |
| 16 | 7S9U|1|A | Large subunit ribosomal RNA | RNA (2436-MER) | Bacillus subtilis | Bacteria | RF02541 | 44SR3C ribosomal particle | Electron microscopy | 3.2 | 2022-03-02 |
| 17 | 6PPF|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Bacterial 45SRbgA ribosomal particle class B | Electron microscopy | 3.4 | 2019-09-18 |
| 18 | 6PVK|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Bacterial 45SRbgA ribosomal particle class A | Electron microscopy | 3.4 | 2019-09-18 |
| 19 | 6HTQ|1|A | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis | Bacteria | RF02541 | Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome | Electron microscopy | 4.5 | 2019-10-23 |
| 20 | 7QGU|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Structure of the B. subtilis disome - stalled 70S ribosome | Electron microscopy | 4.75 | 2022-03-16 |
| 21 | 6PPK|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | RbgA+45SRbgA complex | Electron microscopy | 4.4 | 2019-09-18 |
| 22 | 7QV3|1|V | Large subunit ribosomal RNA | 23S ribosomal RNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S) | Electron microscopy | 5.14 | 2022-03-09 |
| 23 | 7QH4|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis | Bacteria | RF02541 | Structure of the B. subtilis disome - collided 70S ribosome | Electron microscopy | 5.45 | 2022-03-16 |
| 24 | 7ASA|1|A | Large subunit ribosomal RNA | 23S rRNA | Bacillus subtilis subsp. subtilis str. 168 | Bacteria | RF02541 | Bacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | Electron microscopy | 3.5 | 2020-12-23 |
| 25 | 3J3W|1|A | Large subunit ribosomal RNA | ribosome RNA 23S | Bacillus subtilis | Bacteria | RF02541 | Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a) | Electron microscopy | 10.7 | 2013-06-12 |
| 26 | 3J3V|1|A | Large subunit ribosomal RNA | ribosome RNA 23S | Bacillus subtilis | Bacteria | RF02541 | Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a) | Electron microscopy | 13.3 | 2013-06-12 |
Release history
| Release | 3.222 | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2022-03-16 | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_41610.15 | NR_all_41610.14 | 3.222 | (24) 7OPE|1|A, 3J9W|1|BA, 7O5B|1|X, 3J3W|1|A, 7ASA|1|A, 3J3V|1|A, 7AS9|1|A, 7AS8|1|A, 7AQD|1|A, 7AQC|1|A, 6TPQ|1|U, 6TNN|1|U, 6PVK|1|A, 6PPK|1|A, 6PPF|1|A, 7SAE|1|A, 6HTQ|1|A, 7S9U|1|A, 7QV3|1|V, 6HA8|1|A, 7QV2|1|V, 6HA1|1|A, 7QV1|1|V, 5NJT|1|U | (2) 7QGU|1|A, 7QH4|1|A | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_41610.15 | NR_all_41610.16 | 3.277 | (26) 6HA1|1|A, 7QH4|1|A, 5NJT|1|U, 7QGU|1|A, 3J9W|1|BA, 7OPE|1|A, 3J3W|1|A, 7O5B|1|X, 3J3V|1|A, 7ASA|1|A, 7AS9|1|A, 7AS8|1|A, 7AQD|1|A, 7AQC|1|A, 6TPQ|1|U, 6TNN|1|U, 6PVK|1|A, 7SAE|1|A, 6PPK|1|A, 7S9U|1|A, 6PPF|1|A, 7QV3|1|V, 6HTQ|1|A, 7QV2|1|V, 6HA8|1|A, 7QV1|1|V | (0) | (1) 8BUU|1|A |
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 | 3J3W|1|A | Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a) | ELECTRON MICROSCOPY | 10.7 | 2685 |
| 2 | 3J3V|1|A | Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a) | ELECTRON MICROSCOPY | 13.3 | 2884 |
| 3 | 7QV2|1|V | Bacillus subtilis collided disome (Collided 70S) | ELECTRON MICROSCOPY | 3.5 | 2887 |
| 4 | 6PPF|1|A | Bacterial 45SRbgA ribosomal particle class B | ELECTRON MICROSCOPY | 3.4 | 2471 |
| 5 | 6PVK|1|A | Bacterial 45SRbgA ribosomal particle class A | ELECTRON MICROSCOPY | 3.4 | 2169 |
| 6 | 7SAE|1|A | 44SR70P Class1 ribosomal particle | ELECTRON MICROSCOPY | 3 | 2434 |
| 7 | 7S9U|1|A | 44SR3C ribosomal particle | ELECTRON MICROSCOPY | 3.2 | 2436 |
| 8 | 6TPQ|1|U | RNase M5 bound to 50S ribosome with precursor 5S rRNA | ELECTRON MICROSCOPY | 3.07 | 2924 |
| 9 | 6TNN|1|U | Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA | ELECTRON MICROSCOPY | 3.07 | 2930 |
| 10 | 7QV3|1|V | Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S) | ELECTRON MICROSCOPY | 5.14 | 2887 |
| 11 | 7QV1|1|V | Bacillus subtilis collided disome (Leading 70S) | ELECTRON MICROSCOPY | 3.5 | 2887 |
| 12 | 7QGU|1|A | Structure of the B. subtilis disome - stalled 70S ribosome | ELECTRON MICROSCOPY | 4.75 | 2923 |
| 13 | 3J9W|1|BA | Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complex | ELECTRON MICROSCOPY | 3.9 | 2923 |
| 14 | 7QH4|1|A | Structure of the B. subtilis disome - collided 70S ribosome | ELECTRON MICROSCOPY | 5.45 | 2923 |
| 15 | 5NJT|1|U | Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. | ELECTRON MICROSCOPY | 3.8 | 2923 |
| 16 | 6PPK|1|A | RbgA+45SRbgA complex | ELECTRON MICROSCOPY | 4.4 | 2658 |
| 17 | 7AQD|1|A | Structure of the bacterial RQC complex (Translocating State) | ELECTRON MICROSCOPY | 3.1 | 2918 |
| 18 | 7AQC|1|A | Structure of the bacterial RQC complex (Decoding State) | ELECTRON MICROSCOPY | 2.99 | 2820 |
| 19 | 7O5B|1|X | Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP bound | ELECTRON MICROSCOPY | 3.33 | 2887 |
| 20 | 6HTQ|1|A | Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosome | ELECTRON MICROSCOPY | 4.5 | 2887 |
| 21 | 6HA1|1|A | Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycin | ELECTRON MICROSCOPY | 3.1 | 2887 |
| 22 | 7AS9|1|A | Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH. | ELECTRON MICROSCOPY | 3.5 | 2812 |
| 23 | 6HA8|1|A | Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosome | ELECTRON MICROSCOPY | 3.5 | 2887 |
| 24 | 7OPE|1|A | RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement) | ELECTRON MICROSCOPY | 3.2 | 2814 |
| 25 | 7AS8|1|A | Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | ELECTRON MICROSCOPY | 2.9 | 2812 |
| 26 | 7ASA|1|A | Bacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabO | ELECTRON MICROSCOPY | 3.5 | 82 |