Equivalence class NR_3.5_52752.17 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 8GLP|1|L7 (rep) | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure) | Electron microscopy | 1.67 | 2023-04-19 |
| 2 | 8A3D|1|B | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound | Electron microscopy | 1.67 | 2023-03-08 |
| 3 | 7OW7|1|B | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | EIF6-bound large subunit of the human ribosome | Electron microscopy | 2.2 | 2022-10-05 |
| 4 | 8G5Y|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) | Electron microscopy | 2.29 | 2023-04-19 |
| 5 | 7XNY|1|L2 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells | Electron microscopy | 2.5 | 2023-04-05 |
| 6 | 8G60|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) | Electron microscopy | 2.54 | 2023-04-19 |
| 7 | 6ZMI|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex | Electron microscopy | 2.6 | 2020-08-19 |
| 8 | 8G5Z|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state) | Electron microscopy | 2.64 | 2023-04-19 |
| 9 | 6ZM7|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex | Electron microscopy | 2.7 | 2020-07-29 |
| 10 | 7XNX|1|L2 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells | Electron microscopy | 2.7 | 2023-04-05 |
| 11 | 7F5S|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | human delta-METTL18 60S ribosome | Electron microscopy | 2.72 | 2022-06-22 |
| 12 | 8G6J|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) | Electron microscopy | 2.8 | 2023-04-19 |
| 13 | 6XA1|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Structure of a drug-like compound stalled human translation termination complex | Electron microscopy | 2.8 | 2020-10-07 |
| 14 | 6Y6X|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Tetracenomycin X bound to the human ribosome | Electron microscopy | 2.8 | 2020-07-08 |
| 15 | 6Z6N|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) | Electron microscopy | 2.9 | 2020-07-29 |
| 16 | 6QZP|1|L7 | 5S ribosomal RNA | 5S rRNA (120-MER) | Homo sapiens | Eukarya | RF00001 | High-resolution cryo-EM structure of the human 80S ribosome | Electron microscopy | 2.9 | 2019-04-24 |
| 17 | 8G61|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) | Electron microscopy | 2.94 | 2023-04-19 |
| 18 | 6Z6L|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of human CCDC124 bound to 80S ribosomes | Electron microscopy | 3 | 2020-07-29 |
| 19 | 6ZME|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex | Electron microscopy | 3 | 2020-08-12 |
| 20 | 7QVP|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | Electron microscopy | 3 | 2022-10-12 |
| 21 | 7QVP|1|L9 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | Electron microscopy | 3 | 2022-10-12 |
| 22 | 6LQM|1|5 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of a pre-60S ribosomal subunit - state C | Electron microscopy | 3.09 | 2020-08-26 |
| 23 | 6Z6M|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 | Electron microscopy | 3.1 | 2020-07-29 |
| 24 | 6ZMO|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex | Electron microscopy | 3.1 | 2020-08-19 |
| 25 | 6LSR|1|5 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of a pre-60S ribosomal subunit - state B | Electron microscopy | 3.13 | 2020-08-26 |
| 26 | 6LU8|1|5 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of a human pre-60S ribosomal subunit - state A | Electron microscopy | 3.13 | 2020-08-26 |
| 27 | 6OLE|1|E | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs | Electron microscopy | 3.1 | 2019-06-19 |
| 28 | 6Y2L|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Structure of human ribosome in POST state | Electron microscopy | 3 | 2020-04-15 |
| 29 | 6OM0|1|E | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAs | Electron microscopy | 3.1 | 2019-06-19 |
| 30 | 6LSS|1|5 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | Electron microscopy | 3.23 | 2020-08-26 |
| 31 | 6Y0G|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Structure of human ribosome in classical-PRE state | Electron microscopy | 3.2 | 2020-04-15 |
| 32 | 7BHP|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Cryo-EM structure of the human Ebp1 - 80S ribosome | Electron microscopy | 3.3 | 2021-02-03 |
| 33 | 6OLG|1|A4 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) | Electron microscopy | 3.4 | 2019-06-19 |
| 34 | 6OLI|1|E | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC) | Electron microscopy | 3.5 | 2019-06-19 |
| 35 | 6Y57|1|L7 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Structure of human ribosome in hybrid-PRE state | Electron microscopy | 3.5 | 2020-04-15 |
| 36 | 5AJ0|1|A4 | 5S ribosomal RNA | 5S ribosomal RNA | Homo sapiens | Eukarya | RF00001 | Cryo electron microscopy of actively translating human polysomes (POST state). | Electron microscopy | 3.5 | 2015-05-20 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_52752.17 | NR_3.5_52752.16 | 3.279 | (30) 6Y2L|1|L7, 7XNY|1|L2, 6LQM|1|5, 6Z6N|1|L7, 6OLI|1|E, 7F5S|1|L7, 6OLG|1|A4, 7BHP|1|L7, 6Y0G|1|L7, 7XNX|1|L2, 5AJ0|1|A4, 6Z6M|1|L7, 6OLE|1|E, 6ZMO|1|L7, 6XA1|1|L7, 7QVP|1|L9, 6Z6L|1|L7, 6LU8|1|5, 6ZMI|1|L7, 7QVP|1|L7, 6QZP|1|L7, 6Y6X|1|L7, 6LSS|1|5, 6ZME|1|L7, 7OW7|1|B, 6OM0|1|E, 6Y57|1|L7, 8A3D|1|B, 6LSR|1|5, 6ZM7|1|L7 | (6) 8G60|1|L7, 8G6J|1|L7, 8G5Y|1|L7, 8G5Z|1|L7, 8G61|1|L7, 8GLP|1|L7 | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_52752.17 | NR_3.5_52752.18 | 3.291 | (36) 6OM0|1|E, 6ZMO|1|L7, 8GLP|1|L7, 6LSR|1|5, 6Z6L|1|L7, 8A3D|1|B, 6QZP|1|L7, 7F5S|1|L7, 6LSS|1|5, 6Z6M|1|L7, 8G5Y|1|L7, 6XA1|1|L7, 7OW7|1|B, 6LU8|1|5, 6ZM7|1|L7, 8G5Z|1|L7, 6Y0G|1|L7, 7QVP|1|L7, 6OLE|1|E, 6ZME|1|L7, 8G60|1|L7, 6Y57|1|L7, 7QVP|1|L9, 6OLG|1|A4, 6ZMI|1|L7, 8G6J|1|L7, 5AJ0|1|A4, 6Y6X|1|L7, 7XNY|1|L2, 6LQM|1|5, 7BHP|1|L7, 7XNX|1|L2, 6Z6N|1|L7, 6Y2L|1|L7, 8G61|1|L7, 6OLI|1|E | (0) | (13) 8FL3|1|L4, 8FLD|1|L4, 8FL7|1|L4, 8FL0|1|L4, 8FLB|1|L4, 8FL4|1|L4, 8FLE|1|L4, 8FL9|1|L4, 8FL2|1|L4, 8FLC|1|L4, 8FL6|1|L4, 8FLF|1|L4, 8FLA|1|L4 |
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 | 6LSS|1|5 | Cryo-EM structure of a pre-60S ribosomal subunit - state preA | ELECTRON MICROSCOPY | 3.23 | 120 |
| 2 | 6LU8|1|5 | Cryo-EM structure of a human pre-60S ribosomal subunit - state A | ELECTRON MICROSCOPY | 3.13 | 120 |
| 3 | 6LSR|1|5 | Cryo-EM structure of a pre-60S ribosomal subunit - state B | ELECTRON MICROSCOPY | 3.13 | 120 |
| 4 | 6LQM|1|5 | Cryo-EM structure of a pre-60S ribosomal subunit - state C | ELECTRON MICROSCOPY | 3.09 | 120 |
| 5 | 7XNX|1|L2 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells | ELECTRON MICROSCOPY | 2.7 | 120 |
| 6 | 7XNY|1|L2 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells | ELECTRON MICROSCOPY | 2.5 | 120 |
| 7 | 6ZME|1|L7 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex | ELECTRON MICROSCOPY | 3 | 120 |
| 8 | 6ZMO|1|L7 | SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex | ELECTRON MICROSCOPY | 3.1 | 120 |
| 9 | 6ZM7|1|L7 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex | ELECTRON MICROSCOPY | 2.7 | 120 |
| 10 | 6ZMI|1|L7 | SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex | ELECTRON MICROSCOPY | 2.6 | 120 |
| 11 | 6Z6M|1|L7 | Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 | ELECTRON MICROSCOPY | 3.1 | 120 |
| 12 | 6Z6N|1|L7 | Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) | ELECTRON MICROSCOPY | 2.9 | 120 |
| 13 | 6Z6L|1|L7 | Cryo-EM structure of human CCDC124 bound to 80S ribosomes | ELECTRON MICROSCOPY | 3 | 120 |
| 14 | 6Y6X|1|L7 | Tetracenomycin X bound to the human ribosome | ELECTRON MICROSCOPY | 2.8 | 120 |
| 15 | 6XA1|1|L7 | Structure of a drug-like compound stalled human translation termination complex | ELECTRON MICROSCOPY | 2.8 | 120 |
| 16 | 6QZP|1|L7 | High-resolution cryo-EM structure of the human 80S ribosome | ELECTRON MICROSCOPY | 2.9 | 120 |
| 17 | 7OW7|1|B | EIF6-bound large subunit of the human ribosome | ELECTRON MICROSCOPY | 2.2 | 120 |
| 18 | 7F5S|1|L7 | human delta-METTL18 60S ribosome | ELECTRON MICROSCOPY | 2.72 | 120 |
| 19 | 8A3D|1|B | Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound | ELECTRON MICROSCOPY | 1.67 | 120 |
| 20 | 8GLP|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure) | ELECTRON MICROSCOPY | 1.67 | 120 |
| 21 | 8G5Y|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) | ELECTRON MICROSCOPY | 2.29 | 120 |
| 22 | 8G60|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) | ELECTRON MICROSCOPY | 2.54 | 120 |
| 23 | 8G6J|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) | ELECTRON MICROSCOPY | 2.8 | 120 |
| 24 | 8G5Z|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state) | ELECTRON MICROSCOPY | 2.64 | 120 |
| 25 | 8G61|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) | ELECTRON MICROSCOPY | 2.94 | 120 |
| 26 | 7QVP|1|L7 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | ELECTRON MICROSCOPY | 3 | 120 |
| 27 | 6Y2L|1|L7 | Structure of human ribosome in POST state | ELECTRON MICROSCOPY | 3 | 120 |
| 28 | 6Y0G|1|L7 | Structure of human ribosome in classical-PRE state | ELECTRON MICROSCOPY | 3.2 | 120 |
| 29 | 6Y57|1|L7 | Structure of human ribosome in hybrid-PRE state | ELECTRON MICROSCOPY | 3.5 | 120 |
| 30 | 7QVP|1|L9 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | ELECTRON MICROSCOPY | 3 | 120 |
| 31 | 6OM0|1|E | Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAs | ELECTRON MICROSCOPY | 3.1 | 119 |
| 32 | 6OLE|1|E | Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs | ELECTRON MICROSCOPY | 3.1 | 119 |
| 33 | 6OLI|1|E | Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC) | ELECTRON MICROSCOPY | 3.5 | 119 |
| 34 | 6OLG|1|A4 | Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) | ELECTRON MICROSCOPY | 3.4 | 119 |
| 35 | 5AJ0|1|A4 | Cryo electron microscopy of actively translating human polysomes (POST state). | ELECTRON MICROSCOPY | 3.5 | 119 |
| 36 | 7BHP|1|L7 | Cryo-EM structure of the human Ebp1 - 80S ribosome | ELECTRON MICROSCOPY | 3.3 | 120 |