Equivalence class NR_3.5_21280.16 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7JQB|1|A (rep) | Small subunit ribosomal RNA | rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex | Electron microscopy | 2.7 | 2020-12-02 |
| 2 | 6SGC|1|A1 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Rabbit 80S ribosome stalled on a poly(A) tail | Electron microscopy | 2.8 | 2019-12-04 |
| 3 | 6YAL|1|2 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Mammalian 48S late-stage initiation complex with beta-globin mRNA | Electron microscopy | 3 | 2020-04-08 |
| 4 | 6R5Q|1|K | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of XBP1u-paused ribosome nascent chain complex (post-state) | Electron microscopy | 3 | 2019-07-10 |
| 5 | 6ZVK|1|K3 | Small subunit ribosomal RNA | 18S RIBOSOMAL RNA | Oryctolagus cuniculus | Eukarya | RF01960 | The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism | Electron microscopy | 3.49 | 2020-12-23 |
| 6 | 6P5I|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1) | Electron microscopy | 3.1 | 2019-09-18 |
| 7 | 6P5K|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | Electron microscopy | 3.1 | 2019-09-18 |
| 8 | 6P5J|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2) | Electron microscopy | 3.1 | 2019-09-18 |
| 9 | 6P4G|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1) | Electron microscopy | 3.1 | 2019-09-18 |
| 10 | 6R6P|1|K | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of XBP1u-paused ribosome nascent chain complex (rotated state) | Electron microscopy | 3.1 | 2019-07-10 |
| 11 | 6P4H|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2) | Electron microscopy | 3.2 | 2019-09-18 |
| 12 | 6P5N|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1 | Electron microscopy | 3.2 | 2019-09-25 |
| 13 | 6D9J|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | Electron microscopy | 3.2 | 2018-06-06 |
| 14 | 7JQC|1|A | Small subunit ribosomal RNA | rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex | Electron microscopy | 3.3 | 2020-12-02 |
| 15 | 5LZS|1|9 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B | Electron microscopy | 3.31 | 2016-11-30 |
| 16 | 6W2T|1|a | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) | Electron microscopy | 3.36 | 2020-04-22 |
| 17 | 6MTD|1|9 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel) | Electron microscopy | 3.3 | 2018-11-21 |
| 18 | 5LZV|1|9 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1. | Electron microscopy | 3.35 | 2016-11-30 |
| 19 | 6D90|1|2 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. | Electron microscopy | 3.2 | 2018-06-06 |
| 20 | 6YAN|1|2 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Mammalian 48S late-stage translation initiation complex with histone 4 mRNA | Electron microscopy | 3.48 | 2020-04-08 |
| 21 | 6MTC|1|9 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) | Electron microscopy | 3.4 | 2018-11-21 |
| 22 | 6MTE|1|9 | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) | Electron microscopy | 3.4 | 2018-11-21 |
| 23 | 6W2S|1|A | Small subunit ribosomal RNA | 18S rRNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) | Electron microscopy | 3.47 | 2020-04-22 |
| 24 | 6GZ5|1|B1 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3) | Electron microscopy | 3.5 | 2018-12-05 |
| 25 | 5LZZ|1|9 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of the mammalian rescue complex with Pelota and Hbs1l (combined) | Electron microscopy | 3.47 | 2016-11-30 |
| 26 | 3JAH|1|9 | Small subunit ribosomal RNA | 18S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF01960 | Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon | Electron microscopy | 3.45 | 2015-08-12 |
Release history
| Release | 3.159 | 3.160 | 3.161 | 3.162 | 3.163 | 3.164 | 3.165 | 3.166 | 3.167 | 3.168 | 3.169 | 3.170 | 3.171 | 3.172 | 3.173 | 3.174 | 3.175 | 3.176 | 3.177 | 3.178 | 3.179 | 3.180 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2020-12-30 | 2021-01-06 | 2021-01-13 | 2021-01-20 | 2021-01-27 | 2021-02-03 | 2021-02-10 | 2021-02-17 | 2021-02-24 | 2021-03-03 | 2021-03-10 | 2021-03-17 | 2021-03-24 | 2021-03-31 | 2021-04-07 | 2021-04-14 | 2021-04-21 | 2021-04-28 | 2021-05-05 | 2021-05-12 | 2021-05-19 | 2021-05-26 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_21280.16 | NR_3.5_21280.15 | 3.159 | (26) 3JAH|1|9, 5LZS|1|9, 5LZV|1|9, 5LZZ|1|9, 6D90|1|2, 6D9J|1|2, 6GZ5|1|B1, 6MTC|1|9, 6MTD|1|9, 6MTE|1|9, 6P4G|1|2, 6P4H|1|2, 6P5I|1|2, 6P5J|1|2, 6P5K|1|2, 6P5N|1|2, 6R5Q|1|K, 6R6P|1|K, 6SGC|1|A1, 6W2S|1|A, 6W2T|1|a, 6YAL|1|2, 6YAN|1|2, 6ZVK|1|K3, 7JQB|1|A, 7JQC|1|A | (0) | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_21280.16 | NR_3.5_21280.17 | 3.181 | (26) 3JAH|1|9, 5LZS|1|9, 5LZV|1|9, 5LZZ|1|9, 6D90|1|2, 6D9J|1|2, 6GZ5|1|B1, 6MTC|1|9, 6MTD|1|9, 6MTE|1|9, 6P4G|1|2, 6P4H|1|2, 6P5I|1|2, 6P5J|1|2, 6P5K|1|2, 6P5N|1|2, 6R5Q|1|K, 6R6P|1|K, 6SGC|1|A1, 6W2S|1|A, 6W2T|1|a, 6YAL|1|2, 6YAN|1|2, 6ZVK|1|K3, 7JQB|1|A, 7JQC|1|A | (0) | (4) 7O7Y|1|A2, 7O7Z|1|A2, 7O80|1|A2, 7O81|1|A2 |
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 | 6GZ5|1|B1 | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3) | ELECTRON MICROSCOPY | 3.5 | 1708 | |
| 2 | 6ZVK|1|K3 | The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism | ELECTRON MICROSCOPY | 3.49 | 1869 | |
| 3 | 3JAH|1|9 | Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon | ELECTRON MICROSCOPY | 3.45 | 1719 | |
| 4 | 6YAL|1|2 | Mammalian 48S late-stage initiation complex with beta-globin mRNA | ELECTRON MICROSCOPY | 3 | 1743 | |
| 5 | 6YAN|1|2 | Mammalian 48S late-stage translation initiation complex with histone 4 mRNA | ELECTRON MICROSCOPY | 3.48 | 1743 | |
| 6 | 6D90|1|2 | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. | ELECTRON MICROSCOPY | 3.2 | 1697 | |
| 7 | 6P5N|1|2 | Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1 | ELECTRON MICROSCOPY | 3.2 | 1697 | |
| 8 | 6R6P|1|K | Structure of XBP1u-paused ribosome nascent chain complex (rotated state) | ELECTRON MICROSCOPY | 3.1 | 1698 | |
| 9 | 6R5Q|1|K | Structure of XBP1u-paused ribosome nascent chain complex (post-state) | ELECTRON MICROSCOPY | 3 | 1698 | |
| 10 | 6MTC|1|9 | Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) | ELECTRON MICROSCOPY | 3.4 | 1664 | |
| 11 | 5LZS|1|9 | Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin B | ELECTRON MICROSCOPY | 3.31 | 1697 | |
| 12 | 5LZV|1|9 | Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1. | ELECTRON MICROSCOPY | 3.35 | 1698 | |
| 13 | 5LZZ|1|9 | Structure of the mammalian rescue complex with Pelota and Hbs1l (combined) | ELECTRON MICROSCOPY | 3.47 | 1698 | |
| 14 | 6SGC|1|A1 | Rabbit 80S ribosome stalled on a poly(A) tail | ELECTRON MICROSCOPY | 2.8 | 1697 | |
| 15 | 7JQB|1|A | SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex | ELECTRON MICROSCOPY | 2.7 | 1697 | |
| 16 | 7JQC|1|A | SARS-CoV-2 Nsp1, CrPV IRES and rabbit 40S ribosome complex | ELECTRON MICROSCOPY | 3.3 | 1697 | |
| 17 | 6P4H|1|2 | Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2) | ELECTRON MICROSCOPY | 3.2 | 1697 | |
| 18 | 6P4G|1|2 | Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1) | ELECTRON MICROSCOPY | 3.1 | 1697 | |
| 19 | 6P5K|1|2 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3) | ELECTRON MICROSCOPY | 3.1 | 1697 | |
| 20 | 6P5I|1|2 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1) | ELECTRON MICROSCOPY | 3.1 | 1697 | |
| 21 | 6P5J|1|2 | Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2) | ELECTRON MICROSCOPY | 3.1 | 1697 | |
| 22 | 6MTE|1|9 | Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) | ELECTRON MICROSCOPY | 3.4 | 1664 | |
| 23 | 6MTD|1|9 | Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel) | ELECTRON MICROSCOPY | 3.3 | 1692 | |
| 24 | 6W2S|1|A | Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1) | ELECTRON MICROSCOPY | 3.47 | 1697 | |
| 25 | 6W2T|1|a | Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2) | ELECTRON MICROSCOPY | 3.36 | 1697 | |
| 26 | 6D9J|1|2 | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | ELECTRON MICROSCOPY | 3.2 | 1697 |
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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