RNA 3D Hub //

Equivalence class NR_4.0_76703.10 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
15E81|1|1K (rep)Transfer RNAmRNA, tRNA-LysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-ray diffraction2.95722016-01-27
25EL6|1|1LTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycinX-ray diffraction3.1732016-01-27
35IB8|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-siteX-ray diffraction3.13722016-05-25
45EL4|1|1KTransfer RNAmRNA, tRNA-LysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first positionX-ray diffraction3.15692016-01-27
55IB7|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycinX-ray diffraction2.99722016-05-25
65E7K|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-siteX-ray diffraction3.2712016-01-27
75EL4|1|1LTransfer RNAmRNA, tRNA-LysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first positionX-ray diffraction3.15742016-01-27
85EL6|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycinX-ray diffraction3.1692016-01-27
95EL7|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycinX-ray diffraction3.15692016-01-27
105E81|1|1LTransfer RNAmRNA, tRNA-LysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-ray diffraction2.95692016-01-27
115E7K|1|1LTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-siteX-ray diffraction3.2732016-01-27
125EL7|1|1LTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycinX-ray diffraction3.15732016-01-27
135IB7|1|1LTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycinX-ray diffraction2.99662016-05-25
145EL5|1|1KTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second positionX-ray diffraction3.15692016-01-27
155EL5|1|1LTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second positionX-ray diffraction3.15742016-01-27
167N1P|1|PtTransfer RNAmRNA, tRNAEscherichia coli K-12BacteriaRF00005Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformationElectron microscopy2.33762021-07-14
178BF7|1|5Transfer RNADipeptidyl A-site tRNA(Lys), mRNAEscherichia coli K-12BacteriaRF00005Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteElectron microscopy2.33762023-08-16
187N2U|1|PtTransfer RNAmRNA, tRNAEscherichia coli K-12BacteriaRF00005Elongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformationElectron microscopy2.53762021-07-14
198BH4|1|5Transfer RNADipeptidyl A-site tRNA(Lys), mRNAEscherichia coli K-12BacteriaRF00005Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteElectron microscopy2.62762023-08-16
207N30|1|PtTransfer RNAmRNA, tRNAEscherichia coli K-12BacteriaRF00005Elongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformationElectron microscopy2.66762021-07-14
217N31|1|PtTransfer RNAmRNA, tRNAEscherichia coli K-12BacteriaRF00005Elongating 70S ribosome complex in a post-translocation (POST) conformationElectron microscopy2.69762021-07-14
227N2C|1|PtTransfer RNAChains: mR, Chains: PtEscherichia coliBacteriaRF00005Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2)Electron microscopy2.72762021-07-14
238BHJ|1|5Transfer RNADipeptidyl A-site tRNA(Lys), mRNAEscherichia coli K-12BacteriaRF00005Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteElectron microscopy2.81762023-08-16
247ZTA|1|PTR1Transfer RNAmRNA, tRNA-LysEscherichia coli K-12BacteriaRF00005Structure of an Escherichia coli 70S ribosome stalled by Tetracenomycin X during translation of an MAAAPQK(C) peptideElectron microscopy2.7732023-04-12
258BHN|1|5Transfer RNADipeptidyl A-site tRNA(Lys), mRNAEscherichia coli K-12BacteriaRF00005Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteElectron microscopy2.85762023-08-16
268FOM|1|QVTransfer RNAmRNA, P-site tRNA^Lys(SUU)Escherichia coliBacteriaRF00005Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P siteX-ray diffraction3.58742023-03-29
275JTE|1|AWTransfer RNAA-site Lysine tRNA Lysine, mRNAEscherichia coliBacteriaRF00005Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNAElectron microscopy3.6742016-07-20
288FON|1|QVTransfer RNAmRNA, P-site tRNA^Lys(SUU)Escherichia coliBacteriaRF00005Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P siteX-ray diffraction3.64742023-03-29
298FON|1|XVTransfer RNAA-site ASL^Phe, mRNA, P-site tRNA^Lys(SUU)Escherichia coliBacteriaRF00005Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P siteX-ray diffraction3.64742023-03-29
308FOM|1|XVTransfer RNAmRNA, P-site tRNA^Lys(SUU)Escherichia coliBacteriaRF00005Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P siteX-ray diffraction3.58742023-03-29
315UYQ|1|YTransfer RNAmRNA, tRNALysEscherichia coliBacteriaRF0000570S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc)Electron microscopy3.8762017-06-07
325UYP|1|YTransfer RNAtRNALysEscherichia coliBacteriaRF0000570S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc)Electron microscopy3.9762017-06-07
335UYN|1|YTransfer RNAtRNALysEscherichia coliBacteriaRF0000570S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc)Electron microscopy4762017-06-07
347D6Z|1|4Transfer RNAA-site tRNAEscherichia coliBacteriaRF00005Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factorElectron microscopy3.4662021-04-07

Release history

Release3.3783.3793.3803.3813.382
Date2025-03-132025-03-192025-03-262025-04-022025-04-09

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
15EL5|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second positionX-RAY DIFFRACTION3.1569
25EL5|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second positionX-RAY DIFFRACTION3.1574
35EL7|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycinX-RAY DIFFRACTION3.1573
45E81|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9569
55IB7|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycinX-RAY DIFFRACTION2.9966
65EL4|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first positionX-RAY DIFFRACTION3.1574
75EL6|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycinX-RAY DIFFRACTION3.173
85E7K|1|1LStructure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-siteX-RAY DIFFRACTION3.273
95EL6|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycinX-RAY DIFFRACTION3.169
105EL4|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first positionX-RAY DIFFRACTION3.1569
115E7K|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-siteX-RAY DIFFRACTION3.271
125IB7|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycinX-RAY DIFFRACTION2.9972
135E81|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9572
145IB8|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-siteX-RAY DIFFRACTION3.1372
155EL7|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycinX-RAY DIFFRACTION3.1569
165JTE|1|AWCryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNAELECTRON MICROSCOPY3.674
177D6Z|1|4Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factorELECTRON MICROSCOPY3.466
187N1P|1|PtElongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformationELECTRON MICROSCOPY2.3376
197N30|1|PtElongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformationELECTRON MICROSCOPY2.6676
207N2U|1|PtElongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformationELECTRON MICROSCOPY2.5376
217N2C|1|PtElongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2)ELECTRON MICROSCOPY2.7276
227N31|1|PtElongating 70S ribosome complex in a post-translocation (POST) conformationELECTRON MICROSCOPY2.6976
238FOM|1|QVCrystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P siteX-RAY DIFFRACTION3.5874
248FON|1|XVCrystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P siteX-RAY DIFFRACTION3.6474
258FON|1|QVCrystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P siteX-RAY DIFFRACTION3.6474
268FOM|1|XVCrystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P siteX-RAY DIFFRACTION3.5874
277ZTA|1|PTR1Structure of an Escherichia coli 70S ribosome stalled by Tetracenomycin X during translation of an MAAAPQK(C) peptideELECTRON MICROSCOPY2.773
288BHN|1|5Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteELECTRON MICROSCOPY2.8576
298BF7|1|5Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteELECTRON MICROSCOPY2.3376
308BH4|1|5Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteELECTRON MICROSCOPY2.6276
318BHJ|1|5Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-siteELECTRON MICROSCOPY2.8176
325UYN|1|Y70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc)ELECTRON MICROSCOPY476
335UYP|1|Y70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc)ELECTRON MICROSCOPY3.976
345UYQ|1|Y70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc)ELECTRON MICROSCOPY3.876

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.


Coloring options:

Copyright 2025 BGSU RNA group. Page generated in 0.0113 s