RNA 3D Hub //

Equivalence class NR_3.5_24191.5 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19Q87|1|6 (rep)A-site tRNAEscherichia coli BPrinciples of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+Electron microscopy1.5522025-05-14
27QIW|1|stRNASolanum lycopersicumSpecific features and methylation sites of a plant ribosome. 60S ribosomal subunit.Electron microscopy2.3522022-07-13
37QIZ|1|stRNASolanum lycopersicumSpecific features and methylation sites of a plant 80S ribosomeElectron microscopy2.3822022-08-03
47K00|1|5E-site tRNAEscherichia coliStructure of the Bacterial Ribosome at 2 Angstrom ResolutionElectron microscopy1.9822020-09-23
59R3A|1|5E-site tRNAEscherichia coliStructure of Stalled Beta-Galactosidase 70S Ribosome Nascent ChainElectron microscopy2.8622026-01-28
61VY6|1|AWCytidine-Puromycinsynthetic constructCrystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.X-ray diffraction2.922014-08-20
711BQ|1|5E-site tRNAEscherichia coliEscherichia coli 70S ribosome containing an evolved 16S rRNA (EC-S3.5)Electron microscopy322026-04-08
81VY6|1|CWCytidine-Puromycinsynthetic constructCrystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.X-ray diffraction2.922014-08-20
94A3G|1|PTRANSCRIPT RNA 5'-R(*CP*AP)-3'Saccharomyces cerevisiaeRNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybridX-ray diffraction3.522012-02-08
1011DG|1|5E-site tRNAEscherichia coliChimeric Escherichia coli 70S ribosome containing an evolved Vibrio cholerae 16S rRNA (VC-S4.4)Electron microscopy322026-04-08
117NBU|1|WE-site tRNAEscherichia coli K-12Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.Electron microscopy3.1122022-03-02
123J9M|1|uE-site tRNAHomo sapiensStructure of the human mitochondrial ribosome (class 1)Electron microscopy3.522015-04-15
135MMI|1|zE-site tRNASpinacia oleraceaStructure of the large subunit of the chloroplast ribosomeElectron microscopy3.222017-01-11
148AYE|1|5E-site tRNAEscherichia coliE. coli 70S ribosome bound to thermorubin and fMet-tRNAElectron microscopy1.9622023-03-01
158QOA|1|5E-site tRNAEscherichia coli BW25113Structure of SecM-stalled Escherichia coli 70S ribosomeElectron microscopy222024-03-20

Release history

Release4.34
Date2026-04-08

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
18QOA|1|5Structure of SecM-stalled Escherichia coli 70S ribosomeELECTRON MICROSCOPY22
211DG|1|5Chimeric Escherichia coli 70S ribosome containing an evolved Vibrio cholerae 16S rRNA (VC-S4.4)ELECTRON MICROSCOPY32
31VY6|1|AWCrystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.X-RAY DIFFRACTION2.92
43J9M|1|uStructure of the human mitochondrial ribosome (class 1)ELECTRON MICROSCOPY3.52
54A3G|1|PRNA Polymerase II initial transcribing complex with a 2nt DNA-RNA hybridX-RAY DIFFRACTION3.52
61VY6|1|CWCrystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.X-RAY DIFFRACTION2.92
77QIZ|1|sSpecific features and methylation sites of a plant 80S ribosomeELECTRON MICROSCOPY2.382
88AYE|1|5E. coli 70S ribosome bound to thermorubin and fMet-tRNAELECTRON MICROSCOPY1.962
97NBU|1|WStructure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.ELECTRON MICROSCOPY3.112
109Q87|1|6Principles of ion binding to RNA inferred from the analysis of a 1.55 Angstrom resolution bacterial ribosome structure - Part I: Mg2+ELECTRON MICROSCOPY1.552
119R3A|1|5Structure of Stalled Beta-Galactosidase 70S Ribosome Nascent ChainELECTRON MICROSCOPY2.862
127K00|1|5Structure of the Bacterial Ribosome at 2 Angstrom ResolutionELECTRON MICROSCOPY1.982
137QIW|1|sSpecific features and methylation sites of a plant ribosome. 60S ribosomal subunit.ELECTRON MICROSCOPY2.352
1411BQ|1|5Escherichia coli 70S ribosome containing an evolved 16S rRNA (EC-S3.5)ELECTRON MICROSCOPY32
155MMI|1|zStructure of the large subunit of the chloroplast ribosomeELECTRON MICROSCOPY3.22

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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