RNA 3D Hub //

Equivalence class NR_all_69813.8 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16OF1|1|1w (rep)Transfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-ray diffraction2.8732019-04-17
25IBB|1|1KTransfer RNAmRNA, tRNAValEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-ray diffraction2.96722016-05-25
36CAE|1|1yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-ray diffraction2.6742018-04-18
46O97|1|1wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-ray diffraction2.75732019-04-17
56OF1|1|1yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-ray diffraction2.8732019-04-17
66BY1|1|AWTransfer RNAMessenger RNA, Valine-specific transfer RNAEscherichia coliBacteriaRF00005E. coli pH03H9 complexX-ray diffraction3.94762019-02-27
76OF1|1|2wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-ray diffraction2.8732019-04-17
86O97|1|1yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-ray diffraction2.75732019-04-17
96ND6|1|1yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-ray diffraction2.85742019-02-20
106BY1|1|BWTransfer RNAMessenger RNA, Valine-specific transfer RNAEscherichia coliBacteriaRF00005E. coli pH03H9 complexX-ray diffraction3.94762019-02-27
115IBB|1|3LTransfer RNAtRNAValEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-ray diffraction2.96712016-05-25
126CAE|1|1wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-ray diffraction2.6732018-04-18
136BY1|1|BVTransfer RNAMessenger RNA, Valine-specific transfer RNAEscherichia coliBacteriaRF00005E. coli pH03H9 complexX-ray diffraction3.94762019-02-27
146BY1|1|AVTransfer RNAMessenger RNA, Valine-specific transfer RNAEscherichia coliBacteriaRF00005E. coli pH03H9 complexX-ray diffraction3.94762019-02-27
156OF1|1|2yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-ray diffraction2.8732019-04-17
166CAE|1|2yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-ray diffraction2.6732018-04-18
176ND6|1|1wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-ray diffraction2.85732019-02-20
186CAE|1|2wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-ray diffraction2.6732018-04-18
196O97|1|2yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-ray diffraction2.75732019-04-17
205IBB|1|3KTransfer RNAtRNAValEscherichia coliBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-ray diffraction2.96702016-05-25
216ND6|1|2yTransfer RNAA-site and E-site tRNAsEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-ray diffraction2.85732019-02-20
226O97|1|2wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-ray diffraction2.75732019-04-17
236ND6|1|2wTransfer RNAA-site and E-site tRNAs, mRNAEscherichia coliBacteriaRF00005Crystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-ray diffraction2.85732019-02-20
246N1D|1|BPTNTransfer RNAP-tRNAEscherichia coliBacteriaRF00005X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid StateX-ray diffraction3.2762019-04-03
256N1D|1|APTNTransfer RNAmRNA, P-tRNAEscherichia coliBacteriaRF00005X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid StateX-ray diffraction3.2762019-04-03
266BY1|1|AYTransfer RNAMessenger RNA, Valine-specific transfer RNAEscherichia coliBacteriaRF00005E. coli pH03H9 complexX-ray diffraction3.94762019-02-27
277K00|1|YTransfer RNAA-site tRNA-val, mRNAEscherichia coliBacteriaRF00005Structure of the Bacterial Ribosome at 2 Angstrom ResolutionElectron microscopy1.98742020-09-23
284V7A|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4)Electron microscopy9762014-07-09
294V6Y|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a)Electron microscopy12762014-07-09
304V75|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1)Electron microscopy12762014-07-09
314V6Z|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b)Electron microscopy12762014-07-09
324V72|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4)Electron microscopy13762014-07-09
334V73|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a)Electron microscopy15762014-07-09
344V79|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)Electron microscopy15762014-07-09
354V70|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3)Electron microscopy17762014-07-09
364V76|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a)Electron microscopy17762014-07-09
374V77|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b)Electron microscopy17762014-07-09
384V74|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF0000570S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)Electron microscopy17762014-07-09
394V78|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)Electron microscopy20762014-07-09
404V71|1|A1Transfer RNA5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3', fMet-Val-tRNA-ValEscherichia coliBacteriaRF00005E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2)Electron microscopy20762014-07-09
412K4C|1|ATransfer RNA76-MEREscherichia coliBacteriaRF00005tRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS dataSolution NMR, solution scattering762008-12-09

Release history

Release3.1453.1463.1473.1483.1493.1503.1513.1523.1533.1543.1553.1563.1573.1583.1593.1603.1613.1623.1633.1643.1653.1663.1673.1683.1693.1703.1713.1723.1733.1743.1753.1763.1773.1783.179
Date2020-09-232020-09-302020-10-072020-10-142020-10-212020-10-282020-11-042020-11-112020-11-182020-11-252020-12-022020-12-092020-12-162020-12-232020-12-302021-01-062021-01-132021-01-202021-01-272021-02-032021-02-102021-02-172021-02-242021-03-032021-03-102021-03-172021-03-242021-03-312021-04-072021-04-142021-04-212021-04-282021-05-052021-05-122021-05-19

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_all_69813.8NR_all_69813.73.145(40) 2K4C|1|A, 4V6Y|1|A1, 4V6Z|1|A1, 4V70|1|A1, 4V71|1|A1, 4V72|1|A1, 4V73|1|A1, 4V74|1|A1, 4V75|1|A1, 4V76|1|A1, 4V77|1|A1, 4V78|1|A1, 4V79|1|A1, 4V7A|1|A1, 5IBB|1|1K, 5IBB|1|3K, 5IBB|1|3L, 6BY1|1|AV, 6BY1|1|AW, 6BY1|1|AY, 6BY1|1|BV, 6BY1|1|BW, 6CAE|1|1w, 6CAE|1|1y, 6CAE|1|2w, 6CAE|1|2y, 6N1D|1|APTN, 6N1D|1|BPTN, 6ND6|1|1w, 6ND6|1|1y, 6ND6|1|2w, 6ND6|1|2y, 6O97|1|1w, 6O97|1|1y, 6O97|1|2w, 6O97|1|2y, 6OF1|1|1w, 6OF1|1|1y, 6OF1|1|2w, 6OF1|1|2y(1) 7K00|1|Y(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_all_69813.8NR_all_69813.93.180(41) 2K4C|1|A, 4V6Y|1|A1, 4V6Z|1|A1, 4V70|1|A1, 4V71|1|A1, 4V72|1|A1, 4V73|1|A1, 4V74|1|A1, 4V75|1|A1, 4V76|1|A1, 4V77|1|A1, 4V78|1|A1, 4V79|1|A1, 4V7A|1|A1, 5IBB|1|1K, 5IBB|1|3K, 5IBB|1|3L, 6BY1|1|AV, 6BY1|1|AW, 6BY1|1|AY, 6BY1|1|BV, 6BY1|1|BW, 6CAE|1|1w, 6CAE|1|1y, 6CAE|1|2w, 6CAE|1|2y, 6N1D|1|APTN, 6N1D|1|BPTN, 6ND6|1|1w, 6ND6|1|1y, 6ND6|1|2w, 6ND6|1|2y, 6O97|1|1w, 6O97|1|1y, 6O97|1|2w, 6O97|1|2y, 6OF1|1|1w, 6OF1|1|1y, 6OF1|1|2w, 6OF1|1|2y, 7K00|1|Y(0) (1) 7B5K|1|9

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
14V71|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2)ELECTRON MICROSCOPY2076
26ND6|1|1wCrystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-RAY DIFFRACTION2.8573
36O97|1|1wCrystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-RAY DIFFRACTION2.7573
46OF1|1|1wCrystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-RAY DIFFRACTION2.873
56OF1|1|2wCrystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-RAY DIFFRACTION2.873
66CAE|1|1wCrystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-RAY DIFFRACTION2.673
76CAE|1|2wCrystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-RAY DIFFRACTION2.673
86O97|1|2wCrystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-RAY DIFFRACTION2.7573
96ND6|1|2wCrystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-RAY DIFFRACTION2.8573
107K00|1|YStructure of the Bacterial Ribosome at 2 Angstrom ResolutionELECTRON MICROSCOPY1.9874
116BY1|1|AVE. coli pH03H9 complexX-RAY DIFFRACTION3.9476
126BY1|1|BVE. coli pH03H9 complexX-RAY DIFFRACTION3.9476
136BY1|1|BWE. coli pH03H9 complexX-RAY DIFFRACTION3.9476
146BY1|1|AWE. coli pH03H9 complexX-RAY DIFFRACTION3.9476
154V73|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a)ELECTRON MICROSCOPY1576
165IBB|1|1KStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-RAY DIFFRACTION2.9672
174V72|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4)ELECTRON MICROSCOPY1376
184V79|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b)ELECTRON MICROSCOPY1576
194V6Y|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a)ELECTRON MICROSCOPY1276
204V6Z|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b)ELECTRON MICROSCOPY1276
214V78|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a)ELECTRON MICROSCOPY2076
226ND6|1|1yCrystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-RAY DIFFRACTION2.8574
236OF1|1|1yCrystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-RAY DIFFRACTION2.873
246CAE|1|1yCrystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-RAY DIFFRACTION2.674
256O97|1|1yCrystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-RAY DIFFRACTION2.7573
266O97|1|2yCrystal structure of the Thermus thermophilus 70S ribosome in complex with propylamycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.75A resolutionX-RAY DIFFRACTION2.7573
276ND6|1|2yCrystal structure of the Thermus thermophilus 70S ribosome in complex with erythromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.85A resolutionX-RAY DIFFRACTION2.8573
286CAE|1|2yCrystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolutionX-RAY DIFFRACTION2.673
296OF1|1|2yCrystal structure of the Thermus thermophilus 70S ribosome in complex with dirithromycin and bound to mRNA and A-, P-, and E-site tRNAs at 2.80A resolutionX-RAY DIFFRACTION2.873
305IBB|1|3LStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-RAY DIFFRACTION2.9671
315IBB|1|3KStructure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-siteX-RAY DIFFRACTION2.9670
326N1D|1|APTNX-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid StateX-RAY DIFFRACTION3.276
336N1D|1|BPTNX-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into a Chimeric Hybrid StateX-RAY DIFFRACTION3.276
344V70|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3)ELECTRON MICROSCOPY1776
356BY1|1|AYE. coli pH03H9 complexX-RAY DIFFRACTION3.9476
364V75|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1)ELECTRON MICROSCOPY1276
374V7A|1|A1E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4)ELECTRON MICROSCOPY976
384V76|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a)ELECTRON MICROSCOPY1776
394V77|1|A1E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b)ELECTRON MICROSCOPY1776
404V74|1|A170S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b)ELECTRON MICROSCOPY1776
412K4C|1|AtRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS dataSOLUTION NMR, SOLUTION SCATTERING76

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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