RNA 3D Hub //

Equivalence class NR_3.0_06650.49 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18SCB|1|5+ 8SCB|1|8 (rep)Large subunit ribosomal RNA + 5.8S ribosomal RNA28S_rRNA, 5.8S_rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Terminating ribosome with SRI-41315Electron microscopy2.536862023-12-27
27O7Z|1|B5+ 7O7Z|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)Electron microscopy2.439202021-06-02
38RJB|1|K+ 8RJB|1|vLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4Electron microscopy2.6924336992024-01-24
48RJD|1|K+ 8RJD|1|vLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2Electron microscopy2.7857436992024-01-24
58RJC|1|K+ 8RJC|1|vLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1Electron microscopy2.9006136992024-01-24
69RHU|1|A3+ 9RHU|1|C3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequenceElectron microscopy2.6539202026-01-21
78B6C|1|5+ 8B6C|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147Electron microscopy2.7937702023-02-22
88B5L|1|5+ 8B5L|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complexElectron microscopy2.8637702023-03-01
99YQ0|1|5+ 9YQ0|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Vacant ribosome with P-site tRNA, substate 2, Structure IbElectron microscopy2.937522025-12-17
109YQ1|1|5+ 9YQ1|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Vacant ribosome with P-site tRNA, substate 3, Structure IcElectron microscopy2.937522025-12-17
119YPZ|1|5+ 9YPZ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Vacant ribosome with P-site tRNA, substate 1, Structure IaElectron microscopy2.937522025-12-24
128VVQ|1|WA+ 8VVQ|1|YALarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsElectron microscopy2.737342025-07-30
139BDL|1|A28S+ 9BDL|1|A58SLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF0000280S ribosome with angiogeninElectron microscopy2.837082024-07-24
149YPW|1|5+ 9YPW|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVElectron microscopy2.937522025-12-31
159YPY|1|5+ 9YPY|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Ribosome with accommodated A-site tRNA, Structure VElectron microscopy337522025-12-24
169YPG|1|5+ 9YPG|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIElectron microscopy337522025-12-31
178BPO|1|A1+ 8BPO|1|C1Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure 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 microscopy2.836942023-07-05
189YPO|1|5+ 9YPO|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy337522025-12-17
199YPS|1|5+ 9YPS|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy337522025-12-17
209QQA|1|B5+ 9QQA|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Ternary complex of translating ribosome, NAC and NMT1Electron microscopy2.838622025-07-16
219YPV|1|5+ 9YPV|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy337522025-12-17
228P2K|1|B5+ 8P2K|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Ternary complex of translating ribosome, NAC and METAP1Electron microscopy2.939202023-07-19
237UCK|1|5+ 7UCK|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28s rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF0000280S translation initiation complex with ac4c(-1) mRNA and HarringtonineElectron microscopy2.836972022-06-01
247TOR|1|A28S+ 7TOR|1|A58SLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20Electron microscopy2.937032022-05-25
258VVP|1|WA+ 8VVP|1|YALarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Codon sampling state obtained from Anisomycin-treated mammalian ribosomesElectron microscopy2.937342025-07-30
269MR4|1|5+ 9MR4|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002NAC: Ribosome nascent chain complex(Oxa1L)Electron microscopy2.6536202025-08-20
279NDP|1|5+ 9NDP|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of stalled ribosome and nascent chain in complex with NMT2 and NACElectron microscopy2.8236852025-09-10
287OBR|1|5+ 7OBR|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002RNC-SRP early complexElectron microscopy2.836492021-07-21
299Q7Q|1|5+ 9Q7Q|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002ABCE1-eRF1-RNC-AMD1CElectron microscopy2.8635952026-03-04
306R5Q|1|5+ 6R5Q|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of XBP1u-paused ribosome nascent chain complex (post-state)Electron microscopy336942019-07-10
318VVT|1|WA+ 8VVT|1|YALarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian ribosomes bound to Anisomycin in the rotated conformationElectron microscopy2.936922025-07-30
327QWQ|1|5+ 7QWQ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Ternary complex of ribosome nascent chain with SRP and NACElectron microscopy2.8336492022-03-16
337QWR|1|5+ 7QWR|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NACElectron microscopy2.936492022-03-09
347O7Y|1|B5+ 7O7Y|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)Electron microscopy2.239202021-06-02
357ZJW|1|L5+ 7ZJW|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome as it decodes the Sec-UGA codonElectron microscopy2.839202022-10-19
367O80|1|B5+ 7O80|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery siteElectron microscopy2.939202021-06-02
376SGC|1|54+ 6SGC|1|84Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome stalled on a poly(A) tailElectron microscopy2.837542019-12-04
387OYD|1|5+ 7OYD|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bElectron microscopy2.335022022-07-20

Release history

Release4.29
Date2026-03-04

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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.

#SViewPDBTitleMethodResolution#NTs
17QWR|1|5+ 7QWR|1|8Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NACELECTRON MICROSCOPY2.93649
27QWQ|1|5+ 7QWQ|1|8Ternary complex of ribosome nascent chain with SRP and NACELECTRON MICROSCOPY2.833649
37OBR|1|5+ 7OBR|1|8RNC-SRP early complexELECTRON MICROSCOPY2.83649
49RHU|1|A3+ 9RHU|1|C3Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequenceELECTRON MICROSCOPY2.653920
57O80|1|B5+ 7O80|1|B8Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery siteELECTRON MICROSCOPY2.93920
68VVP|1|WA+ 8VVP|1|YACodon sampling state obtained from Anisomycin-treated mammalian ribosomesELECTRON MICROSCOPY2.93734
78VVQ|1|WA+ 8VVQ|1|YACodon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsELECTRON MICROSCOPY2.73734
88SCB|1|5+ 8SCB|1|8Terminating ribosome with SRI-41315ELECTRON MICROSCOPY2.53686
96R5Q|1|5+ 6R5Q|1|8Structure of XBP1u-paused ribosome nascent chain complex (post-state)ELECTRON MICROSCOPY33694
108BPO|1|A1+ 8BPO|1|C1Structure 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 MICROSCOPY2.83694
119YPV|1|5+ 9YPV|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY33752
129YPO|1|5+ 9YPO|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY33752
139YPS|1|5+ 9YPS|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY33752
149YPW|1|5+ 9YPW|1|8GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.93752
159YPG|1|5+ 9YPG|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY33752
168RJD|1|K+ 8RJD|1|vStructure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 2ELECTRON MICROSCOPY2.785743699
178RJC|1|K+ 8RJC|1|vStructure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-TRAP, open conformation 1ELECTRON MICROSCOPY2.900613699
188RJB|1|K+ 8RJB|1|vStructure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4ELECTRON MICROSCOPY2.692433699
199YPY|1|5+ 9YPY|1|8Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY33752
209YPZ|1|5+ 9YPZ|1|8Vacant ribosome with P-site tRNA, substate 1, Structure IaELECTRON MICROSCOPY2.93752
219YQ1|1|5+ 9YQ1|1|8Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.93752
229YQ0|1|5+ 9YQ0|1|8Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.93752
237UCK|1|5+ 7UCK|1|880S translation initiation complex with ac4c(-1) mRNA and HarringtonineELECTRON MICROSCOPY2.83697
248B6C|1|5+ 8B6C|1|8Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147ELECTRON MICROSCOPY2.793770
258B5L|1|5+ 8B5L|1|8Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complexELECTRON MICROSCOPY2.863770
267OYD|1|5+ 7OYD|1|8Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bELECTRON MICROSCOPY2.33502
278VVT|1|WA+ 8VVT|1|YAMammalian ribosomes bound to Anisomycin in the rotated conformationELECTRON MICROSCOPY2.93692
286SGC|1|54+ 6SGC|1|84Rabbit 80S ribosome stalled on a poly(A) tailELECTRON MICROSCOPY2.83754
299NDP|1|5+ 9NDP|1|8Structure of stalled ribosome and nascent chain in complex with NMT2 and NACELECTRON MICROSCOPY2.823685
309MR4|1|5+ 9MR4|1|8NAC: Ribosome nascent chain complex(Oxa1L)ELECTRON MICROSCOPY2.653620
317TOR|1|A28S+ 7TOR|1|A58SMammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20ELECTRON MICROSCOPY2.93703
329BDL|1|A28S+ 9BDL|1|A58S80S ribosome with angiogeninELECTRON MICROSCOPY2.83708
337O7Y|1|B5+ 7O7Y|1|B8Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)ELECTRON MICROSCOPY2.23920
347O7Z|1|B5+ 7O7Z|1|B8Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)ELECTRON MICROSCOPY2.43920
358P2K|1|B5+ 8P2K|1|B8Ternary complex of translating ribosome, NAC and METAP1ELECTRON MICROSCOPY2.93920
369QQA|1|B5+ 9QQA|1|B8Ternary complex of translating ribosome, NAC and NMT1ELECTRON MICROSCOPY2.83862
377ZJW|1|L5+ 7ZJW|1|L8Rabbit 80S ribosome as it decodes the Sec-UGA codonELECTRON MICROSCOPY2.83920
389Q7Q|1|5+ 9Q7Q|1|8ABCE1-eRF1-RNC-AMD1CELECTRON MICROSCOPY2.863595

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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