Equivalence class NR_3.0_10255.48 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7O7Z|1|B7 (rep) | 5S ribosomal RNA | 5S | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot) | Electron microscopy | 2.4 | 120 | 2021-06-02 |
| 2 | 8SCB|1|7 | 5S ribosomal RNA | 5S_rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Terminating ribosome with SRI-41315 | Electron microscopy | 2.5 | 120 | 2023-12-27 |
| 3 | 9RHU|1|B3 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence | Electron microscopy | 2.65 | 119 | 2026-01-21 |
| 4 | 8RJB|1|u | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 | Electron microscopy | 2.69243 | 120 | 2024-01-24 |
| 5 | 8RJD|1|u | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 | Electron microscopy | 2.78574 | 120 | 2024-01-24 |
| 6 | 8RJC|1|u | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 | Electron microscopy | 2.90061 | 120 | 2024-01-24 |
| 7 | 8BPO|1|B1 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER) | Electron microscopy | 2.8 | 120 | 2023-07-05 |
| 8 | 9YQ1|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Vacant ribosome with P-site tRNA, substate 3, Structure Ic | Electron microscopy | 2.9 | 119 | 2025-12-17 |
| 9 | 9YPZ|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Vacant ribosome with P-site tRNA, substate 1, Structure Ia | Electron microscopy | 2.9 | 119 | 2025-12-24 |
| 10 | 9YPW|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IV | Electron microscopy | 2.9 | 119 | 2025-12-31 |
| 11 | 9YQ0|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Vacant ribosome with P-site tRNA, substate 2, Structure Ib | Electron microscopy | 2.9 | 119 | 2025-12-17 |
| 12 | 9YPG|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure III | Electron microscopy | 3 | 119 | 2025-12-31 |
| 13 | 8VVQ|1|XA | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasets | Electron microscopy | 2.7 | 119 | 2025-07-30 |
| 14 | 9QQA|1|B7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Ternary complex of translating ribosome, NAC and NMT1 | Electron microscopy | 2.8 | 120 | 2025-07-16 |
| 15 | 9YPO|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIa | Electron microscopy | 3 | 119 | 2025-12-17 |
| 16 | 9MR4|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | NAC: Ribosome nascent chain complex(Oxa1L) | Electron microscopy | 2.65 | 120 | 2025-08-20 |
| 17 | 9YPS|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIb | Electron microscopy | 3 | 119 | 2025-12-17 |
| 18 | 9YPY|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Ribosome with accommodated A-site tRNA, Structure V | Electron microscopy | 3 | 119 | 2025-12-24 |
| 19 | 9BDL|1|A5S | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | 80S ribosome with angiogenin | Electron microscopy | 2.8 | 120 | 2024-07-24 |
| 20 | 8B6C|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147 | Electron microscopy | 2.79 | 120 | 2023-02-22 |
| 21 | 9YPV|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IId | Electron microscopy | 3 | 119 | 2025-12-17 |
| 22 | 8B5L|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complex | Electron microscopy | 2.86 | 120 | 2023-03-01 |
| 23 | 8P2K|1|B7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Ternary complex of translating ribosome, NAC and METAP1 | Electron microscopy | 2.9 | 119 | 2023-07-19 |
| 24 | 7UCK|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine | Electron microscopy | 2.8 | 120 | 2022-06-01 |
| 25 | 8VVP|1|XA | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Codon sampling state obtained from Anisomycin-treated mammalian ribosomes | Electron microscopy | 2.9 | 119 | 2025-07-30 |
| 26 | 7OBR|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | RNC-SRP early complex | Electron microscopy | 2.8 | 120 | 2021-07-21 |
| 27 | 9NDP|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC | Electron microscopy | 2.82 | 120 | 2025-09-10 |
| 28 | 7TOR|1|A5S | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 | Electron microscopy | 2.9 | 120 | 2022-05-25 |
| 29 | 6R5Q|1|7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of XBP1u-paused ribosome nascent chain complex (post-state) | Electron microscopy | 3 | 120 | 2019-07-10 |
| 30 | 8VVT|1|XA | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Mammalian ribosomes bound to Anisomycin in the rotated conformation | Electron microscopy | 2.9 | 120 | 2025-07-30 |
| 31 | 7QWR|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NAC | Electron microscopy | 2.9 | 120 | 2022-03-09 |
| 32 | 7QWQ|1|7 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Ternary complex of ribosome nascent chain with SRP and NAC | Electron microscopy | 2.83 | 120 | 2022-03-16 |
| 33 | 7O7Y|1|B7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution) | Electron microscopy | 2.2 | 120 | 2021-06-02 |
| 34 | 7ZJW|1|L7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome as it decodes the Sec-UGA codon | Electron microscopy | 2.8 | 119 | 2022-10-19 |
| 35 | 7O80|1|B7 | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site | Electron microscopy | 2.9 | 119 | 2021-06-02 |
| 36 | 6SGC|1|74 | 5S ribosomal RNA | 5S ribosomal RNA | Oryctolagus cuniculus | Eukarya | RF00001 | Rabbit 80S ribosome stalled on a poly(A) tail | Electron microscopy | 2.8 | 119 | 2019-12-04 |
| 37 | 7OYD|1|K | 5S ribosomal RNA | 5S rRNA | Oryctolagus cuniculus | Eukarya | RF00001 | Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b | Electron microscopy | 2.3 | 119 | 2022-07-20 |
Release history
| Release | 4.23 |
|---|---|
| Date | 2026-01-21 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
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Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
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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 | #NTs |
|---|---|---|---|---|---|---|
| 1 | 7QWR|1|7 | Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NAC | ELECTRON MICROSCOPY | 2.9 | 120 | |
| 2 | 7QWQ|1|7 | Ternary complex of ribosome nascent chain with SRP and NAC | ELECTRON MICROSCOPY | 2.83 | 120 | |
| 3 | 7OBR|1|7 | RNC-SRP early complex | ELECTRON MICROSCOPY | 2.8 | 120 | |
| 4 | 9MR4|1|7 | NAC: Ribosome nascent chain complex(Oxa1L) | ELECTRON MICROSCOPY | 2.65 | 120 | |
| 5 | 7TOR|1|A5S | Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20 | ELECTRON MICROSCOPY | 2.9 | 120 | |
| 6 | 9NDP|1|7 | Structure of stalled ribosome and nascent chain in complex with NMT2 and NAC | ELECTRON MICROSCOPY | 2.82 | 120 | |
| 7 | 6R5Q|1|7 | Structure of XBP1u-paused ribosome nascent chain complex (post-state) | ELECTRON MICROSCOPY | 3 | 120 | |
| 8 | 8VVT|1|XA | Mammalian ribosomes bound to Anisomycin in the rotated conformation | ELECTRON MICROSCOPY | 2.9 | 120 | |
| 9 | 7UCK|1|7 | 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine | ELECTRON MICROSCOPY | 2.8 | 120 | |
| 10 | 8B5L|1|7 | Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complex | ELECTRON MICROSCOPY | 2.86 | 120 | |
| 11 | 8B6C|1|7 | Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147 | ELECTRON MICROSCOPY | 2.79 | 120 | |
| 12 | 8VVP|1|XA | Codon sampling state obtained from Anisomycin-treated mammalian ribosomes | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 13 | 8VVQ|1|XA | Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasets | ELECTRON MICROSCOPY | 2.7 | 119 | |
| 14 | 8BPO|1|B1 | Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 (TTC5) and S-phase Cyclin A Associated Protein residing in the ER (SCAPER) | ELECTRON MICROSCOPY | 2.8 | 120 | |
| 15 | 9BDL|1|A5S | 80S ribosome with angiogenin | ELECTRON MICROSCOPY | 2.8 | 120 | |
| 16 | 7OYD|1|K | Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b | ELECTRON MICROSCOPY | 2.3 | 119 | |
| 17 | 7ZJW|1|L7 | Rabbit 80S ribosome as it decodes the Sec-UGA codon | ELECTRON MICROSCOPY | 2.8 | 119 | |
| 18 | 9YPS|1|7 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIb | ELECTRON MICROSCOPY | 3 | 119 | |
| 19 | 9YPG|1|7 | GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure III | ELECTRON MICROSCOPY | 3 | 119 | |
| 20 | 9YPO|1|7 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIa | ELECTRON MICROSCOPY | 3 | 119 | |
| 21 | 9YPV|1|7 | GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IId | ELECTRON MICROSCOPY | 3 | 119 | |
| 22 | 9YPY|1|7 | Ribosome with accommodated A-site tRNA, Structure V | ELECTRON MICROSCOPY | 3 | 119 | |
| 23 | 9YQ0|1|7 | Vacant ribosome with P-site tRNA, substate 2, Structure Ib | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 24 | 9YPZ|1|7 | Vacant ribosome with P-site tRNA, substate 1, Structure Ia | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 25 | 9YQ1|1|7 | Vacant ribosome with P-site tRNA, substate 3, Structure Ic | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 26 | 9YPW|1|7 | GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IV | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 27 | 8SCB|1|7 | Terminating ribosome with SRI-41315 | ELECTRON MICROSCOPY | 2.5 | 120 | |
| 28 | 8P2K|1|B7 | Ternary complex of translating ribosome, NAC and METAP1 | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 29 | 7O80|1|B7 | Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery site | ELECTRON MICROSCOPY | 2.9 | 119 | |
| 30 | 9RHU|1|B3 | Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence | ELECTRON MICROSCOPY | 2.65 | 119 | |
| 31 | 7O7Y|1|B7 | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution) | ELECTRON MICROSCOPY | 2.2 | 120 | |
| 32 | 7O7Z|1|B7 | Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot) | ELECTRON MICROSCOPY | 2.4 | 120 | |
| 33 | 6SGC|1|74 | Rabbit 80S ribosome stalled on a poly(A) tail | ELECTRON MICROSCOPY | 2.8 | 119 | |
| 34 | 8RJB|1|u | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4 | ELECTRON MICROSCOPY | 2.69243 | 120 | |
| 35 | 8RJC|1|u | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1 | ELECTRON MICROSCOPY | 2.90061 | 120 | |
| 36 | 8RJD|1|u | Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2 | ELECTRON MICROSCOPY | 2.78574 | 120 | |
| 37 | 9QQA|1|B7 | Ternary complex of translating ribosome, NAC and NMT1 | ELECTRON MICROSCOPY | 2.8 | 120 |
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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