Equivalence class NR_3.0_52752.18 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 | 8FL7|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State J2) | Electron microscopy | 2.55 | 2023-07-12 |
| 8 | 8FLE|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State L2) | Electron microscopy | 2.48 | 2023-07-12 |
| 9 | 8FLB|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State K2) | Electron microscopy | 2.55 | 2023-07-12 |
| 10 | 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 |
| 11 | 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 |
| 12 | 8FL6|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State J1) | Electron microscopy | 2.62 | 2023-07-12 |
| 13 | 8FLA|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State K1) | Electron microscopy | 2.63 | 2023-07-12 |
| 14 | 8FLD|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State L1) | Electron microscopy | 2.58 | 2023-07-12 |
| 15 | 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 |
| 16 | 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 |
| 17 | 8FL3|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State I2) | Electron microscopy | 2.53 | 2023-07-12 |
| 18 | 7F5S|1|L7 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | human delta-METTL18 60S ribosome | Electron microscopy | 2.72 | 2022-06-22 |
| 19 | 8FLF|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State L3) | Electron microscopy | 2.65 | 2023-07-12 |
| 20 | 8FL9|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State J3) | Electron microscopy | 2.75 | 2023-07-12 |
| 21 | 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 |
| 22 | 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 |
| 23 | 8FLC|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State K3) | Electron microscopy | 2.76 | 2023-07-12 |
| 24 | 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 |
| 25 | 8FL2|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State I1) | Electron microscopy | 2.67 | 2023-07-12 |
| 26 | 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 |
| 27 | 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 |
| 28 | 8FL0|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nucleolar pre-60S ribosomal subunit (State H) | Electron microscopy | 2.91 | 2023-07-12 |
| 29 | 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 |
| 30 | 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 |
| 31 | 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 |
| 32 | 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 |
| 33 | 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 |
| 34 | 8FL4|1|L4 | 5S ribosomal RNA | 5S rRNA | Homo sapiens | Eukarya | RF00001 | Human nuclear pre-60S ribosomal subunit (State I3) | Electron microscopy | 2.89 | 2023-07-12 |
| 35 | 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.0_52752.18 | NR_3.0_52752.17 | 3.291 | (22) 8G61|1|L7, 6ZM7|1|L7, 7XNY|1|L2, 6XA1|1|L7, 8GLP|1|L7, 7F5S|1|L7, 8G5Y|1|L7, 6Z6L|1|L7, 7QVP|1|L7, 8G60|1|L7, 6ZMI|1|L7, 7XNX|1|L2, 6Y6X|1|L7, 8G6J|1|L7, 7OW7|1|B, 6Z6N|1|L7, 8A3D|1|B, 6QZP|1|L7, 7QVP|1|L9, 6ZME|1|L7, 8G5Z|1|L7, 6Y2L|1|L7 | (13) 8FL4|1|L4, 8FLD|1|L4, 8FL6|1|L4, 8FLE|1|L4, 8FLC|1|L4, 8FL3|1|L4, 8FLB|1|L4, 8FL2|1|L4, 8FLA|1|L4, 8FL0|1|L4, 8FL9|1|L4, 8FLF|1|L4, 8FL7|1|L4 | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.0_52752.18 | NR_3.0_52752.19 | 3.295 | (35) 7XNX|1|L2, 8FL3|1|L4, 8FLB|1|L4, 8G5Y|1|L7, 6Y2L|1|L7, 8GLP|1|L7, 6ZMI|1|L7, 8FLA|1|L4, 6ZME|1|L7, 7QVP|1|L9, 8FLF|1|L4, 8FL2|1|L4, 6XA1|1|L7, 8G6J|1|L7, 8FL9|1|L4, 6ZM7|1|L7, 7QVP|1|L7, 8FLE|1|L4, 8FL0|1|L4, 6QZP|1|L7, 8G61|1|L7, 8FL7|1|L4, 6Z6N|1|L7, 7OW7|1|B, 8FLD|1|L4, 8A3D|1|B, 8G60|1|L7, 8FL6|1|L4, 6Z6L|1|L7, 7F5S|1|L7, 8FLC|1|L4, 7XNY|1|L2, 8G5Z|1|L7, 8FL4|1|L4, 6Y6X|1|L7 | (0) | (3) 8IDY|1|5, 8INF|1|5, 8IDT|1|5 |
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 | 7QVP|1|L9 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | ELECTRON MICROSCOPY | 3 | 120 |
| 2 | 7QVP|1|L7 | Human collided disome (di-ribosome) stalled on XBP1 mRNA | ELECTRON MICROSCOPY | 3 | 120 |
| 3 | 6Y2L|1|L7 | Structure of human ribosome in POST state | ELECTRON MICROSCOPY | 3 | 120 |
| 4 | 8G61|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) | ELECTRON MICROSCOPY | 2.94 | 120 |
| 5 | 8G5Z|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state) | ELECTRON MICROSCOPY | 2.64 | 120 |
| 6 | 8G6J|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) | ELECTRON MICROSCOPY | 2.8 | 120 |
| 7 | 8G60|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) | ELECTRON MICROSCOPY | 2.54 | 120 |
| 8 | 8G5Y|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) | ELECTRON MICROSCOPY | 2.29 | 120 |
| 9 | 8GLP|1|L7 | mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure) | ELECTRON MICROSCOPY | 1.67 | 120 |
| 10 | 8A3D|1|B | Human mature large subunit of the ribosome with eIF6 and homoharringtonine bound | ELECTRON MICROSCOPY | 1.67 | 120 |
| 11 | 7F5S|1|L7 | human delta-METTL18 60S ribosome | ELECTRON MICROSCOPY | 2.72 | 120 |
| 12 | 7OW7|1|B | EIF6-bound large subunit of the human ribosome | ELECTRON MICROSCOPY | 2.2 | 120 |
| 13 | 6QZP|1|L7 | High-resolution cryo-EM structure of the human 80S ribosome | ELECTRON MICROSCOPY | 2.9 | 120 |
| 14 | 6XA1|1|L7 | Structure of a drug-like compound stalled human translation termination complex | ELECTRON MICROSCOPY | 2.8 | 120 |
| 15 | 6Y6X|1|L7 | Tetracenomycin X bound to the human ribosome | ELECTRON MICROSCOPY | 2.8 | 120 |
| 16 | 6Z6L|1|L7 | Cryo-EM structure of human CCDC124 bound to 80S ribosomes | ELECTRON MICROSCOPY | 3 | 120 |
| 17 | 6Z6N|1|L7 | Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) | ELECTRON MICROSCOPY | 2.9 | 120 |
| 18 | 6ZMI|1|L7 | SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex | ELECTRON MICROSCOPY | 2.6 | 120 |
| 19 | 6ZM7|1|L7 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex | ELECTRON MICROSCOPY | 2.7 | 120 |
| 20 | 6ZME|1|L7 | SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex | ELECTRON MICROSCOPY | 3 | 120 |
| 21 | 7XNY|1|L2 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells | ELECTRON MICROSCOPY | 2.5 | 120 |
| 22 | 7XNX|1|L2 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cells | ELECTRON MICROSCOPY | 2.7 | 120 |
| 23 | 8FLF|1|L4 | Human nuclear pre-60S ribosomal subunit (State L3) | ELECTRON MICROSCOPY | 2.65 | 120 |
| 24 | 8FLE|1|L4 | Human nuclear pre-60S ribosomal subunit (State L2) | ELECTRON MICROSCOPY | 2.48 | 120 |
| 25 | 8FLD|1|L4 | Human nuclear pre-60S ribosomal subunit (State L1) | ELECTRON MICROSCOPY | 2.58 | 120 |
| 26 | 8FL9|1|L4 | Human nuclear pre-60S ribosomal subunit (State J3) | ELECTRON MICROSCOPY | 2.75 | 120 |
| 27 | 8FL6|1|L4 | Human nuclear pre-60S ribosomal subunit (State J1) | ELECTRON MICROSCOPY | 2.62 | 120 |
| 28 | 8FL7|1|L4 | Human nuclear pre-60S ribosomal subunit (State J2) | ELECTRON MICROSCOPY | 2.55 | 120 |
| 29 | 8FLB|1|L4 | Human nuclear pre-60S ribosomal subunit (State K2) | ELECTRON MICROSCOPY | 2.55 | 120 |
| 30 | 8FLA|1|L4 | Human nuclear pre-60S ribosomal subunit (State K1) | ELECTRON MICROSCOPY | 2.63 | 120 |
| 31 | 8FLC|1|L4 | Human nuclear pre-60S ribosomal subunit (State K3) | ELECTRON MICROSCOPY | 2.76 | 120 |
| 32 | 8FL4|1|L4 | Human nuclear pre-60S ribosomal subunit (State I3) | ELECTRON MICROSCOPY | 2.89 | 117 |
| 33 | 8FL3|1|L4 | Human nuclear pre-60S ribosomal subunit (State I2) | ELECTRON MICROSCOPY | 2.53 | 117 |
| 34 | 8FL2|1|L4 | Human nuclear pre-60S ribosomal subunit (State I1) | ELECTRON MICROSCOPY | 2.67 | 117 |
| 35 | 8FL0|1|L4 | Human nucleolar pre-60S ribosomal subunit (State H) | ELECTRON MICROSCOPY | 2.91 | 120 |