RNA 3D Hub //

Equivalence class NR_3.5_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
259YPT|1|5+ 9YPT|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 IIcElectron microscopy3.137522025-12-17
2611HV|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
277NWI|1|5+ 7NWI|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA+BlaS, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin SElectron microscopy3.1338182021-07-07
287TOR|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
298VVP|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
3011HE|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
319BDN|1|A28S+ 9BDN|1|A58SLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF0000280S ribosome with angiogenin and tRNAAlaElectron microscopy3.137082024-07-24
327ZJX|1|L5+ 7ZJX|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome programmed with SECIS and SBP2Electron microscopy3.138882022-09-07
339F1B|1|B5+ 9F1B|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/EElectron microscopy3.0138622024-08-21
349MR4|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
357TM3|1|K+ 7TM3|1|vLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass transloconElectron microscopy3.2536992022-10-19
3611HG|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
376P5I|1|5+ 6P5I|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)Electron microscopy3.137452019-09-18
389NDP|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
398BHF|1|A2+ 8BHF|1|C2Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4Electron microscopy3.137542023-09-06
407OBR|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
417O81|1|B5+ 7O81|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknotElectron microscopy3.139202021-06-02
4211JJ|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
436P5K|1|5+ 6P5K|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)Electron microscopy3.137452019-09-18
447UCJ|1|5+ 7UCJ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28s rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S translation initiation complex with mRNA and HarringtonineElectron microscopy3.136492022-06-01
456MTD|1|5+ 6MTD|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)Electron microscopy3.337482018-11-21
467TOQ|1|A25S+ 7TOQ|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 poly-PRElectron microscopy3.138052022-05-25
476MTE|1|5+ 6MTE|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)Electron microscopy3.437482018-11-21
489Q7Q|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
496P5N|1|5+ 6P5N|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1Electron microscopy3.237452019-09-25
506MTC|1|5+ 6MTC|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)Electron microscopy3.437482018-11-21
516R5Q|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
529F1D|1|B5+ 9F1D|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPKElectron microscopy3.2638622024-08-21
537MDZ|1|5+ 7MDZ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF0000280S rabbit ribosome stalled with benzamide-CHXElectron microscopy3.236922021-09-01
548VVT|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
555LZV|1|5+ 5LZV|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.Electron microscopy3.3536942016-11-30
5611KH|1|28+ 11KH|1|58Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S with IFRD2 and LARP1, 40S head-swiveledElectron microscopy3.136932026-09-02
575LZS|1|5+ 5LZS|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BElectron microscopy3.3136942016-11-30
589QQB|1|B5+ 9QQB|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Quaternary complex of a translating ribosome, NAC, NMT1, and NatAElectron microscopy3.4339202025-07-16
595LZZ|1|5+ 5LZZ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)Electron microscopy3.4736942016-11-30
606P5J|1|5+ 6P5J|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)Electron microscopy3.137452019-09-18
616R6P|1|5+ 6R6P|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of XBP1u-paused ribosome nascent chain complex (rotated state)Electron microscopy3.138182019-07-10
628VVR|1|WA+ 8VVR|1|YALarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Post-decoding/Post-hydrolysis state obtained from Anisomycin-treated mammalian ribosomesElectron microscopy3.137342025-07-30
638VVS|1|WA+ 8VVS|1|YALarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Post-decoding post-hydrolysis state obtained from merged datasets of elongation inhibitor-treated mammalian ribosomesElectron microscopy3.137342025-07-30
647QWQ|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
658VFT|1|5+ 8VFT|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Translating 80S rabbit ribosome stalled by emetine with eEF2Electron microscopy3.336852024-12-25
666ZVK|1|e2+ 6ZVK|1|h2Large subunit ribosomal RNA + 5.8S ribosomal RNA28S RIBOSOMAL RNA, 5.8S RIBOSOMAL RNAOryctolagus cuniculusEukaryaRF02543 + RF00002The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanismElectron microscopy3.4940762020-12-23
676D90|1|5+ 6D90|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.Electron microscopy3.237452018-06-06
687NFX|1|5+ 7NFX|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state AElectron microscopy3.236492021-06-02
697QWR|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
708VVV|1|5+ 8VVV|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian ribosomes bound to Anisomycin in the nonrotated conformationElectron microscopy3.136802025-07-30
716D9J|1|5+ 6D9J|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.Electron microscopy3.237452018-06-06
726GZ5|1|A2+ 6GZ5|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)Electron microscopy3.537692018-12-05
733JAH|1|5+ 3JAH|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonElectron microscopy3.4538182015-08-12
747QWS|1|5+ 7QWS|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of ribosome translating beta-tubulin in complex with TTC5 and NACElectron microscopy3.436492022-03-09
756T59|1|54+ 6T59|1|84Large 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 and nascent chain-associated complexElectron microscopy3.1136942019-11-27
767O7Y|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
777ZJW|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
787O80|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
796SGC|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
808BTK|1|B5+ 8BTK|1|B8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the TRAP complex with the Sec translocon and a translating ribosomeElectron microscopy3.539202023-05-24
817OYD|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
829Q1S|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
839Q2P|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
849Q2M|1|5+ 9Q2M|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site Ala-tRNA on NediV ORFElectron microscopy3.336632026-06-17
859Q1Q|1|5+ 9Q1Q|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002NediV IRES (A site) in complex with Rabbit 80S ribosomeElectron microscopy3.537542026-06-17

Release history

Release4.55
Date2026-09-02

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
16D9J|1|5+ 6D9J|1|8Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.ELECTRON MICROSCOPY3.23745
26D90|1|5+ 6D90|1|8Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.ELECTRON MICROSCOPY3.23745
36P5N|1|5+ 6P5N|1|8Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1ELECTRON MICROSCOPY3.23745
48BTK|1|B5+ 8BTK|1|B8Structure of the TRAP complex with the Sec translocon and a translating ribosomeELECTRON MICROSCOPY3.53920
57ZJW|1|L5+ 7ZJW|1|L8Rabbit 80S ribosome as it decodes the Sec-UGA codonELECTRON MICROSCOPY2.83920
69Q1S|1|5+ 9Q1S|1|8NediV IRES (P site) in complex with Rabbit 80S ribosomeELECTRON MICROSCOPY33694
79Q1Q|1|5+ 9Q1Q|1|8NediV IRES (A site) in complex with Rabbit 80S ribosomeELECTRON MICROSCOPY3.53754
87MDZ|1|5+ 7MDZ|1|880S rabbit ribosome stalled with benzamide-CHXELECTRON MICROSCOPY3.23692
96SGC|1|54+ 6SGC|1|84Rabbit 80S ribosome stalled on a poly(A) tailELECTRON MICROSCOPY2.83754
108BHF|1|A2+ 8BHF|1|C2Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4ELECTRON MICROSCOPY3.13754
115LZZ|1|5+ 5LZZ|1|8Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)ELECTRON MICROSCOPY3.473694
127ZJX|1|L5+ 7ZJX|1|L8Rabbit 80S ribosome programmed with SECIS and SBP2ELECTRON MICROSCOPY3.13888
138VFT|1|5+ 8VFT|1|8Translating 80S rabbit ribosome stalled by emetine with eEF2ELECTRON MICROSCOPY3.33685
146P5K|1|5+ 6P5K|1|8Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)ELECTRON MICROSCOPY3.13745
156P5I|1|5+ 6P5I|1|8Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)ELECTRON MICROSCOPY3.13745
166P5J|1|5+ 6P5J|1|8Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)ELECTRON MICROSCOPY3.13745
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
188SCB|1|5+ 8SCB|1|8Terminating ribosome with SRI-41315ELECTRON MICROSCOPY2.53686
199Q2M|1|5+ 9Q2M|1|8Rabbit ribosomal 80S elongation complex with eEF2, partial P site Ala-tRNA, E site Ala-tRNA on NediV ORFELECTRON MICROSCOPY3.33663
209Q2P|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
215LZS|1|5+ 5LZS|1|8Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BELECTRON MICROSCOPY3.313694
225LZV|1|5+ 5LZV|1|8Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.ELECTRON MICROSCOPY3.353694
236R5Q|1|5+ 6R5Q|1|8Structure of XBP1u-paused ribosome nascent chain complex (post-state)ELECTRON MICROSCOPY33694
246T59|1|54+ 6T59|1|84Structure of rabbit 80S ribosome translating beta-tubulin in complex with tetratricopeptide protein 5 and nascent chain-associated complexELECTRON MICROSCOPY3.113694
257TM3|1|K+ 7TM3|1|vStructure of the rabbit 80S ribosome stalled on a 2-TMD Rhodopsin intermediate in complex with the multipass transloconELECTRON MICROSCOPY3.253699
268BPO|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
279YPS|1|5+ 9YPS|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY33752
289YPW|1|5+ 9YPW|1|8GTPBP1*GDP*Phe-tRNA*ribosome in the post-GTP hydrolysis state, Structure IVELECTRON MICROSCOPY2.93752
299YPO|1|5+ 9YPO|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY33752
309YPV|1|5+ 9YPV|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY33752
319YPT|1|5+ 9YPT|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.13752
329YPG|1|5+ 9YPG|1|8GTPBP1*GCP*Phe-tRNA*ribosome in the GTPase activation-like state, Structure IIIELECTRON MICROSCOPY33752
338RJD|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
348RJC|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
3511KH|1|28+ 11KH|1|58Rabbit 80S with IFRD2 and LARP1, 40S head-swiveledELECTRON MICROSCOPY3.13693
3611HE|1|28+ 11HE|1|58Rabbit 60S ribosomal subunit with eEF2 domain IV closedELECTRON MICROSCOPY2.863637
3711HV|1|28+ 11HV|1|58Rabbit 60S ribosomal subunit with eEF2 domain IV openELECTRON MICROSCOPY2.93637
3811IQ|1|28+ 11IQ|1|58Rabbit 80S with eEF2,eIF5A and SERBP1ELECTRON MICROSCOPY2.43649
3911HG|1|28+ 11HG|1|58Rabbit 80S with eEF2,CCDC124,and LARP1,40S-head-swiveledELECTRON MICROSCOPY2.93653
4011JJ|1|28+ 11JJ|1|58Rabbit 80S with eEF2,IFRD2 and LARP1,40S-head-swiveledELECTRON MICROSCOPY2.93653
416MTD|1|5+ 6MTD|1|8Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)ELECTRON MICROSCOPY3.33748
426MTC|1|5+ 6MTC|1|8Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)ELECTRON MICROSCOPY3.43748
436MTE|1|5+ 6MTE|1|8Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)ELECTRON MICROSCOPY3.43748
448VVV|1|5+ 8VVV|1|8Mammalian ribosomes bound to Anisomycin in the nonrotated conformationELECTRON MICROSCOPY3.13680
458VVT|1|WA+ 8VVT|1|YAMammalian ribosomes bound to Anisomycin in the rotated conformationELECTRON MICROSCOPY2.93692
467OYD|1|5+ 7OYD|1|8Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bELECTRON MICROSCOPY2.33502
478B6C|1|5+ 8B6C|1|8Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative CK147ELECTRON MICROSCOPY2.793770
488B5L|1|5+ 8B5L|1|8Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complexELECTRON MICROSCOPY2.863770
497UCK|1|5+ 7UCK|1|880S translation initiation complex with ac4c(-1) mRNA and HarringtonineELECTRON MICROSCOPY2.83697
507UCJ|1|5+ 7UCJ|1|8Mammalian 80S translation initiation complex with mRNA and HarringtonineELECTRON MICROSCOPY3.13649
518VVQ|1|WA+ 8VVQ|1|YACodon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsELECTRON MICROSCOPY2.73734
528VVP|1|WA+ 8VVP|1|YACodon sampling state obtained from Anisomycin-treated mammalian ribosomesELECTRON MICROSCOPY2.93734
538VVS|1|WA+ 8VVS|1|YAPost-decoding post-hydrolysis state obtained from merged datasets of elongation inhibitor-treated mammalian ribosomesELECTRON MICROSCOPY3.13734
548VVR|1|WA+ 8VVR|1|YAPost-decoding/Post-hydrolysis state obtained from Anisomycin-treated mammalian ribosomesELECTRON MICROSCOPY3.13734
559NDP|1|5+ 9NDP|1|8Structure of stalled ribosome and nascent chain in complex with NMT2 and NACELECTRON MICROSCOPY2.823685
569MR4|1|5+ 9MR4|1|8NAC: Ribosome nascent chain complex(Oxa1L)ELECTRON MICROSCOPY2.653620
579BDN|1|A28S+ 9BDN|1|A58S80S ribosome with angiogenin and tRNAAlaELECTRON MICROSCOPY3.13708
589YPY|1|5+ 9YPY|1|8Ribosome with accommodated A-site tRNA, Structure VELECTRON MICROSCOPY33752
599YPZ|1|5+ 9YPZ|1|8Vacant ribosome with P-site tRNA, substate 1, Structure IaELECTRON MICROSCOPY2.93752
609YQ1|1|5+ 9YQ1|1|8Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.93752
619YQ0|1|5+ 9YQ0|1|8Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.93752
629BDL|1|A28S+ 9BDL|1|A58S80S ribosome with angiogeninELECTRON MICROSCOPY2.83708
637TOR|1|A28S+ 7TOR|1|A58SMammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20ELECTRON MICROSCOPY2.93703
649QQA|1|B5+ 9QQA|1|B8Ternary complex of translating ribosome, NAC and NMT1ELECTRON MICROSCOPY2.83862
659QQB|1|B5+ 9QQB|1|B8Quaternary complex of a translating ribosome, NAC, NMT1, and NatAELECTRON MICROSCOPY3.433920
669F1D|1|B5+ 9F1D|1|B8Mammalian quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatA/E-HYPKELECTRON MICROSCOPY3.263862
678P2K|1|B5+ 8P2K|1|B8Ternary complex of translating ribosome, NAC and METAP1ELECTRON MICROSCOPY2.93920
687O7Z|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
697O7Y|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
709F1B|1|B5+ 9F1B|1|B8Mammalian ternary complex of a translating 80S ribosome, NAC and NatA/EELECTRON MICROSCOPY3.013862
717O81|1|B5+ 7O81|1|B8Rabbit 80S ribosome colliding in another ribosome stalled by the SARS-CoV-2 pseudoknotELECTRON MICROSCOPY3.13920
727TOQ|1|A25S+ 7TOQ|1|A58SMammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein poly-PRELECTRON MICROSCOPY3.13805
739Q7Q|1|5+ 9Q7Q|1|8ABCE1-eRF1-RNC-AMD1CELECTRON MICROSCOPY2.863595
747O80|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
759RHU|1|A3+ 9RHU|1|C3Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequenceELECTRON MICROSCOPY2.653920
767QWS|1|5+ 7QWS|1|8Structure of ribosome translating beta-tubulin in complex with TTC5 and NACELECTRON MICROSCOPY3.43649
777QWR|1|5+ 7QWR|1|8Structure of the ribosome-nascent chain containing an ER signal sequence in complex with NACELECTRON MICROSCOPY2.93649
787QWQ|1|5+ 7QWQ|1|8Ternary complex of ribosome nascent chain with SRP and NACELECTRON MICROSCOPY2.833649
797OBR|1|5+ 7OBR|1|8RNC-SRP early complexELECTRON MICROSCOPY2.83649
807NFX|1|5+ 7NFX|1|8Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state AELECTRON MICROSCOPY3.23649
813JAH|1|5+ 3JAH|1|8Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonELECTRON MICROSCOPY3.453818
826R6P|1|5+ 6R6P|1|8Structure of XBP1u-paused ribosome nascent chain complex (rotated state)ELECTRON MICROSCOPY3.13818
836ZVK|1|e2+ 6ZVK|1|h2The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanismELECTRON MICROSCOPY3.494076
847NWI|1|5+ 7NWI|1|8Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin SELECTRON MICROSCOPY3.133818
856GZ5|1|A2+ 6GZ5|1|A3tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.53769

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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