RNA 3D Hub //

Equivalence class NR_3.0_06650.51 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
411IQ|1|28+ 11IQ|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S with eEF2,eIF5A and SERBP1Electron microscopy2.436492026-09-02
58RJD|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
68RJC|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
79RHU|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
88B6C|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
98B5L|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
109YQ0|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
119YQ1|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
129YPZ|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
138VVQ|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
149BDL|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
159YPW|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
169YPY|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
179YPG|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
188BPO|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
199YPO|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
209YPS|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
219QQA|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
229YPV|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
238P2K|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
247UCK|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
2511HV|1|28+ 11HV|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 60S ribosomal subunit with eEF2 domain IV openElectron microscopy2.936372026-09-02
267TOR|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
278VVP|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
2811HE|1|28+ 11HE|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 60S ribosomal subunit with eEF2 domain IV closedElectron microscopy2.8636372026-09-02
299MR4|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
3011HG|1|28+ 11HG|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28s rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveledElectron microscopy2.936532026-09-02
319NDP|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
327OBR|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
3311JJ|1|28+ 11JJ|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveledElectron microscopy2.936532026-09-02
349Q7Q|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
356R5Q|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
368VVT|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
377QWQ|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
387QWR|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
397O7Y|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
407ZJW|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
417O80|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
426SGC|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
437OYD|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
449Q1S|1|5+ 9Q1S|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002NediV IRES (P site) in complex with Rabbit 80S ribosomeElectron microscopy336942026-06-17
459Q2P|1|5+ 9Q2P|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORFElectron microscopy336942026-06-17

Release history

Release4.55
Date2026-09-02

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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
19Q7Q|1|5+ 9Q7Q|1|8ABCE1-eRF1-RNC-AMD1CELECTRON MICROSCOPY2.863595
27O80|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
39RHU|1|A3+ 9RHU|1|C3Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequenceELECTRON MICROSCOPY2.653920
48VVQ|1|WA+ 8VVQ|1|YACodon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsELECTRON MICROSCOPY2.73734
58VVP|1|WA+ 8VVP|1|YACodon sampling state obtained from Anisomycin-treated mammalian ribosomesELECTRON MICROSCOPY2.93734
69YPG|1|5+ 9YPG|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY33752
79YPV|1|5+ 9YPV|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY33752
89YPO|1|5+ 9YPO|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY33752
99YPW|1|5+ 9YPW|1|8GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.93752
109YPS|1|5+ 9YPS|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY33752
119Q2P|1|5+ 9Q2P|1|8Rabbit ribosomal 80S elongation complex with eEF1A, A*/T Ala-tRNA, P site Ala-tRNA, E site Ala-tRNA on NediV ORFELECTRON MICROSCOPY33694
126R5Q|1|5+ 6R5Q|1|8Structure of XBP1u-paused ribosome nascent chain complex (post-state)ELECTRON MICROSCOPY33694
138BPO|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
148SCB|1|5+ 8SCB|1|8Terminating ribosome with SRI-41315ELECTRON MICROSCOPY2.53686
158RJD|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
168RJC|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
178RJB|1|K+ 8RJB|1|vStructure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in complex with Sec61-RAMP4ELECTRON MICROSCOPY2.692433699
1811HE|1|28+ 11HE|1|58Rabbit 60S ribosomal subunit with eEF2 domain IV closedELECTRON MICROSCOPY2.863637
1911HV|1|28+ 11HV|1|58Rabbit 60S ribosomal subunit with eEF2 domain IV openELECTRON MICROSCOPY2.93637
2011IQ|1|28+ 11IQ|1|58Rabbit 80S with eEF2,eIF5A and SERBP1ELECTRON MICROSCOPY2.43649
2111HG|1|28+ 11HG|1|58Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveledELECTRON MICROSCOPY2.93653
2211JJ|1|28+ 11JJ|1|58Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveledELECTRON MICROSCOPY2.93653
238VVT|1|WA+ 8VVT|1|YAMammalian ribosomes bound to Anisomycin in the rotated conformationELECTRON MICROSCOPY2.93692
247OYD|1|5+ 7OYD|1|8Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bELECTRON MICROSCOPY2.33502
258B5L|1|5+ 8B5L|1|8Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complexELECTRON MICROSCOPY2.863770
268B6C|1|5+ 8B6C|1|8Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147ELECTRON MICROSCOPY2.793770
277UCK|1|5+ 7UCK|1|880S translation initiation complex with ac4c(-1) mRNA and HarringtonineELECTRON MICROSCOPY2.83697
286SGC|1|54+ 6SGC|1|84Rabbit 80S ribosome stalled on a poly(A) tailELECTRON MICROSCOPY2.83754
299MR4|1|5+ 9MR4|1|8NAC: Ribosome nascent chain complex(Oxa1L)ELECTRON MICROSCOPY2.653620
309NDP|1|5+ 9NDP|1|8Structure of stalled ribosome and nascent chain in complex with NMT2 and NACELECTRON MICROSCOPY2.823685
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
339YQ0|1|5+ 9YQ0|1|8Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.93752
349YQ1|1|5+ 9YQ1|1|8Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.93752
359YPZ|1|5+ 9YPZ|1|8Vacant ribosome with P-site tRNA, substate 1, Structure IaELECTRON MICROSCOPY2.93752
369YPY|1|5+ 9YPY|1|8Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY33752
379Q1S|1|5+ 9Q1S|1|8NediV IRES (P site) in complex with Rabbit 80S ribosomeELECTRON MICROSCOPY33694
387O7Z|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
397O7Y|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
408P2K|1|B5+ 8P2K|1|B8Ternary complex of translating ribosome, NAC and METAP1ELECTRON MICROSCOPY2.93920
419QQA|1|B5+ 9QQA|1|B8Ternary complex of translating ribosome, NAC and NMT1ELECTRON MICROSCOPY2.83862
427ZJW|1|L5+ 7ZJW|1|L8Rabbit 80S ribosome as it decodes the Sec-UGA codonELECTRON MICROSCOPY2.83920
437OBR|1|5+ 7OBR|1|8RNC-SRP early complexELECTRON MICROSCOPY2.83649
447QWQ|1|5+ 7QWQ|1|8Ternary complex of ribosome nascent chain with SRP and NACELECTRON MICROSCOPY2.833649
457QWR|1|5+ 7QWR|1|8Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NACELECTRON MICROSCOPY2.93649

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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