RNA 3D Hub //

Equivalence class NR_3.0_21280.42 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17O7Z|1|A2 (rep)Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)Electron microscopy2.417702021-06-02
28SCB|1|9Small subunit ribosomal RNA18S_rRNAOryctolagus cuniculusEukaryaRF01960Terminating ribosome with SRI-41315Electron microscopy2.516922023-12-27
37JQB|1|ASmall subunit ribosomal RNArRNAOryctolagus cuniculusEukaryaRF01960SARS-CoV-2 Nsp1 and rabbit 40S ribosome complexElectron microscopy2.716972020-12-02
47UCK|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF0196080S translation initiation complex with ac4c(-1) mRNA and HarringtonineElectron microscopy2.816982022-06-01
58VVQ|1|ZASmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsElectron microscopy2.717162025-07-30
69QQA|1|A2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Ternary complex of translating ribosome, NAC and NMT1Electron microscopy2.817702025-07-16
79BDL|1|A18SSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF0196080S ribosome with angiogeninElectron microscopy2.816912024-07-24
88P2K|1|A2Small subunit ribosomal RNA18s rRNAOryctolagus cuniculusEukaryaRF01960Ternary complex of translating ribosome, NAC and METAP1Electron microscopy2.917702023-07-19
98VVP|1|ZASmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Codon sampling state obtained from Anisomycin-treated mammalian ribosomesElectron microscopy2.917162025-07-30
107TOR|1|A18SSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Mammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20Electron microscopy2.916912022-05-25
119NDP|1|KSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of stalled ribosome and nascent chain in complex with NMT2 and NACElectron microscopy2.8216982025-09-10
129MR4|1|KSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960NAC: Ribosome nascent chain complex(Oxa1L)Electron microscopy2.6516912025-08-20
136YAL|1|2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Mammalian 48S late-stage initiation complex with beta-globin mRNAElectron microscopy317442020-04-08
146R5Q|1|KSmall subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of XBP1u-paused ribosome nascent chain complex (post-state)Electron microscopy316982019-07-10
158VVT|1|ZASmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Mammalian ribosomes bound to Anisomycin in the rotated conformationElectron microscopy2.916982025-07-30
167O7Y|1|A2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)Electron microscopy2.217702021-06-02
177ZJW|1|S2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome as it decodes the Sec-UGA codonElectron microscopy2.817702022-10-19
187O80|1|A2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery siteElectron microscopy2.917702021-06-02
196SGC|1|A1Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome stalled on a poly(A) tailElectron microscopy2.816972019-12-04
207OYD|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bElectron microscopy2.316982022-07-20

Release history

Release4.4
Date2025-09-10

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
16YAL|1|2Mammalian 48S late-stage initiation complex with beta-globin mRNAELECTRON MICROSCOPY31744
28SCB|1|9Terminating ribosome with SRI-41315ELECTRON MICROSCOPY2.51692
37ZJW|1|S2Rabbit 80S ribosome as it decodes the Sec-UGA codonELECTRON MICROSCOPY2.81770
49QQA|1|A2Ternary complex of translating ribosome, NAC and NMT1ELECTRON MICROSCOPY2.81770
58P2K|1|A2Ternary complex of translating ribosome, NAC and METAP1ELECTRON MICROSCOPY2.91770
67O7Z|1|A2Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot)ELECTRON MICROSCOPY2.41770
77O7Y|1|A2Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (high resolution)ELECTRON MICROSCOPY2.21770
87O80|1|A2Rabbit 80S ribosome in complex with eRF1 and ABCE1 stalled at the STOP codon in the mutated SARS-CoV-2 slippery siteELECTRON MICROSCOPY2.91770
98VVQ|1|ZACodon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from merged datasetsELECTRON MICROSCOPY2.71716
108VVP|1|ZACodon sampling state obtained from Anisomycin-treated mammalian ribosomesELECTRON MICROSCOPY2.91716
119BDL|1|A18S80S ribosome with angiogeninELECTRON MICROSCOPY2.81691
127TOR|1|A18SMammalian 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein GR20ELECTRON MICROSCOPY2.91691
136R5Q|1|KStructure of XBP1u-paused ribosome nascent chain complex (post-state)ELECTRON MICROSCOPY31698
149NDP|1|KStructure of stalled ribosome and nascent chain in complex with NMT2 and NACELECTRON MICROSCOPY2.821698
159MR4|1|KNAC: Ribosome nascent chain complex(Oxa1L)ELECTRON MICROSCOPY2.651691
167UCK|1|980S translation initiation complex with ac4c(-1) mRNA and HarringtonineELECTRON MICROSCOPY2.81698
176SGC|1|A1Rabbit 80S ribosome stalled on a poly(A) tailELECTRON MICROSCOPY2.81697
187JQB|1|ASARS-CoV-2 Nsp1 and rabbit 40S ribosome complexELECTRON MICROSCOPY2.71697
197OYD|1|9Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1bELECTRON MICROSCOPY2.31698
208VVT|1|ZAMammalian ribosomes bound to Anisomycin in the rotated conformationELECTRON MICROSCOPY2.91698

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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