RNA 3D Hub //

Equivalence class NR_3.5_56101.8 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17Z20|1|v (rep)Transfer RNAPro-tRNAEscherichia coliBacteriaRF0000570S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chainElectron microscopy2.29772022-08-10
29WNQ|1|ZTransfer RNAA-tRNA(PRO),P-tRNA(PRO), mRNAEscherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptideElectron microscopy2.59772025-10-22
39WNQ|1|YTransfer RNAA-tRNA(PRO),P-tRNA(PRO), mRNAEscherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptideElectron microscopy2.59772025-10-22
48ZEJ|1|YTransfer RNAmRNA, P-site tRNA (Chain Y), A-site tRNA-PRO (Chain Z)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptideElectron microscopy2.69772025-06-18
59WNR|1|ZTransfer RNAmRNA, P-tRNA(PRO), A-tRNA(PRO)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorElectron microscopy2.76772025-10-22
69WNR|1|YTransfer RNAmRNA, P-tRNA(PRO), A-tRNA(PRO)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorElectron microscopy2.76772025-10-22
75MGP|1|xTransfer RNAmRNA, P-site tRNAEscherichia coliBacteriaRF00005Structural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAsElectron microscopy3.1772016-12-14
86SZS|1|xTransfer RNAmRNA, P-site tRNA-Pro(CGG)Escherichia coliBacteriaRF00005Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilisElectron microscopy3.06772019-12-04
98ZEJ|1|ZTransfer RNAmRNA, P-site tRNA (Chain Y), A-site tRNA-PRO (Chain Z)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptideElectron microscopy2.69772025-06-18
107ZP8|1|vTransfer RNAPro-tRNAEscherichia coliBacteriaRF0000570S E. coli ribosome with a stalled filamin domain 5 nascent chainElectron microscopy2.2762022-08-10
116ENU|1|xTransfer RNAmRNA, Proline tRNAEscherichia coliBacteriaRF00005Polyproline-stalled ribosome in the presence of elongation-factor P (EF-P)Electron microscopy3.1772017-11-22
128ZFI|1|YTransfer RNAmRNA, P-site tRNA (Chain-Y), A-site tRNA-PRO (Chain-Z)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorElectron microscopy2.9772025-06-18
138ZFI|1|ZTransfer RNAmRNA, P-site tRNA (Chain-Y), A-site tRNA-PRO (Chain-Z)Escherichia coliBacteriaRF00005Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorElectron microscopy2.9772025-06-18
146ENF|1|xTransfer RNAproline tRNA, RNA (5'-R(P*CP*CP*G)-3'), mRNAEscherichia coliBacteriaRF00005Cryo-EM structure of a polyproline-stalled ribosome in the absence of EF-PElectron microscopy3.2772017-11-22
157CPJ|1|9Transfer RNAmRNA, P/P tRNAEscherichia coliBacteriaRF00005ycbZ-stalled 70S ribosomeElectron microscopy3.3772021-12-08
167ZOD|1|vTransfer RNAPro-tRNAEscherichia coliBacteriaRF0000570S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobiaElectron microscopy2.56772022-08-10
176NUO|1|XVTransfer RNAmRNA, P-site tRNA-ProEscherichia coliBacteriaRF00005Modified tRNA(Pro) bound to Thermus thermophilus 70S (cognate)X-ray diffraction3.2772020-10-14
186NUO|1|QVTransfer RNAmRNA, P-site tRNA-ProEscherichia coliBacteriaRF00005Modified tRNA(Pro) bound to Thermus thermophilus 70S (cognate)X-ray diffraction3.2772020-10-14
197O1C|1|B8Transfer RNAmRNA, P-site tRNA-ProEscherichia coli K-12BacteriaRF00005Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in response to L-tryptophanElectron microscopy2.6772021-09-01
207O1A|1|B8Transfer RNAmRNA, P-site tRNA-ProEscherichia coli K-12BacteriaRF00005Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophanElectron microscopy2.4772021-09-01
217O19|1|B8Transfer RNAmRNA, P-site tRNA-ProEscherichia coli K-12BacteriaRF00005Cryo-EM structure of an Escherichia coli TnaC-ribosome complex stalled in response to L-tryptophanElectron microscopy2.9772021-09-01

Release history

Release4.10
Date2025-10-22

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
17ZOD|1|v70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobiaELECTRON MICROSCOPY2.5677
27Z20|1|v70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chainELECTRON MICROSCOPY2.2977
37O1A|1|B8Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophanELECTRON MICROSCOPY2.477
47O1C|1|B8Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome-RF2 complex stalled in response to L-tryptophanELECTRON MICROSCOPY2.677
57O19|1|B8Cryo-EM structure of an Escherichia coli TnaC-ribosome complex stalled in response to L-tryptophanELECTRON MICROSCOPY2.977
66SZS|1|xRelease factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilisELECTRON MICROSCOPY3.0677
75MGP|1|xStructural basis for ArfA-RF2 mediated translation termination on stop-codon lacking mRNAsELECTRON MICROSCOPY3.177
87CPJ|1|9ycbZ-stalled 70S ribosomeELECTRON MICROSCOPY3.377
96ENF|1|xCryo-EM structure of a polyproline-stalled ribosome in the absence of EF-PELECTRON MICROSCOPY3.277
106ENU|1|xPolyproline-stalled ribosome in the presence of elongation-factor P (EF-P)ELECTRON MICROSCOPY3.177
116NUO|1|XVModified tRNA(Pro) bound to Thermus thermophilus 70S (cognate)X-RAY DIFFRACTION3.277
126NUO|1|QVModified tRNA(Pro) bound to Thermus thermophilus 70S (cognate)X-RAY DIFFRACTION3.277
139WNQ|1|YStructure of E.coli ribosome in complex with an engineered arrest peptideELECTRON MICROSCOPY2.5977
148ZEJ|1|YStructure of E.coli ribosome in complex with an engineered arrest peptideELECTRON MICROSCOPY2.6977
159WNR|1|YStructure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorELECTRON MICROSCOPY2.7677
168ZFI|1|YStructure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorELECTRON MICROSCOPY2.977
179WNQ|1|ZStructure of E.coli ribosome in complex with an engineered arrest peptideELECTRON MICROSCOPY2.5977
188ZEJ|1|ZStructure of E.coli ribosome in complex with an engineered arrest peptideELECTRON MICROSCOPY2.6977
199WNR|1|ZStructure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorELECTRON MICROSCOPY2.7677
208ZFI|1|ZStructure of E.coli ribosome in complex with an engineered arrest peptide and trigger factorELECTRON MICROSCOPY2.977
217ZP8|1|v70S E. coli ribosome with a stalled filamin domain 5 nascent chainELECTRON MICROSCOPY2.276

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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