RNA 3D Hub //

Equivalence class NR_20.0_20721.8 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
15E81|1|2K (rep)Transfer RNAmRNA, tRNA-fMetThermus thermophilusBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-ray diffraction2.95772016-01-27
25J8B|1|xTransfer RNAmRNA, P-site tRNAThermus thermophilusBacteriaRF00005Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosomeX-ray diffraction2.6772016-05-25
34V95|1|AVTransfer RNAmRNA, P-site fMet-tRNAThermus thermophilusBacteriaRF00005Crystal structure of YAEJ bound to the 70S ribosomeX-ray diffraction3.2772014-07-09
44V7J|1|AvTransfer RNARNA (5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*A*AP*AP*AP*AP*UP*GP*(OMU)P*(A2M)P*(OMG)P*AP*AP*AP*A)-3'), RNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.3772014-07-09
54V9B|1|ACTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.1772014-07-09
64V7J|1|BvTransfer RNARNA (5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*A*AP*AP*AP*AP*UP*GP*(OMU)P*(A2M)P*(OMG)P*AP*AP*AP*A)-3'), RNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.3772014-07-09
75E81|1|2LTransfer RNAmRNA, tRNA-fMetThermus thermophilusBacteriaRF00005Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-ray diffraction2.95772016-01-27
84V9B|1|CCTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.1772014-07-09
94V95|1|CVTransfer RNAmRNA, P-site fMet-tRNAThermus thermophilusBacteriaRF00005Crystal structure of YAEJ bound to the 70S ribosomeX-ray diffraction3.2772014-07-09
104V7K|1|BvTransfer RNARNA (5'-R(*A*AP*GP*UP*AP*AP*AP*AP*AP*UP*GP*UP*A*(CCC))-3'), RNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.6772014-07-09
114V7K|1|AvTransfer RNARNA (5'-R(*A*AP*GP*UP*AP*AP*AP*AP*AP*UP*GP*UP*A*(CCC))-3'), RNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.6772014-07-09
124WT8|1|C4Transfer RNAmRNA, P site trNAThermus thermophilusBacteriaRF00005Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complexX-ray diffraction3.4772015-01-21
134V9A|1|ACTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tetracycline.X-ray diffraction3.3772014-07-09
144L47|1|XVTransfer RNAA-site ASL SufA6, messenger RNA, P-site tRNA fMetThermus thermophilusBacteriaRF00005Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-ray diffraction3.22772014-08-06
154V7K|1|BwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.6772014-07-09
164L47|1|QVTransfer RNAA-site ASL SufA6, messenger RNA, P-site tRNA fMetThermus thermophilusBacteriaRF00005Crystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-ray diffraction3.22772014-08-06
174V7K|1|AwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.6772014-07-09
184V9A|1|CCTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tetracycline.X-ray diffraction3.3772014-07-09
194V7J|1|AwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.3772014-07-09
204V7J|1|BwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.3772014-07-09
214V9B|1|CDTransfer RNATRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.1772014-07-09
224V4J|1|zTransfer RNAMRNA, P-site tRNAfMETThermus thermophilusBacteriaRF00005Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.X-ray diffraction3.83772014-07-09
234V9B|1|ADTransfer RNATRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.1772014-07-09
244V5A|1|AWTransfer RNATRNA-FMETEscherichia coliBacteriaRF00005Structure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-ray diffraction3.5772014-07-09
254V5A|1|CWTransfer RNATRNA-FMETEscherichia coliBacteriaRF00005Structure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-ray diffraction3.5772014-07-09
264V8X|1|AVTransfer RNA5'-R(*GP*GP*CP*AP*AP*GP*GP*AP*GP*GP*UP*AP*AP*AP *AP*AP*UP*G U2M A2M A2MP*AP*AP*AP*A)-3', transfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.35772014-07-09
274V9N|1|CWTransfer RNAmessenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3'), P-site tRNA-fMetThermus thermophilusBacteriaRF00005Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-ray diffraction3.4772014-07-09
284V8X|1|CVTransfer RNABACTERIAL TOXIN YOEB, transfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.35772014-07-09
294V9N|1|AWTransfer RNAmessenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3'), P-site tRNA-fMetThermus thermophilusBacteriaRF00005Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-ray diffraction3.4772014-07-09
304V8U|1|CWTransfer RNARNAThermus thermophilusBacteriaRF00005Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-ray diffraction3.7772014-07-09
314V8U|1|AWTransfer RNARNAThermus thermophilusBacteriaRF00005Crystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-ray diffraction3.7772014-07-09
324V8X|1|CWTransfer RNAtransfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.35772014-07-09
334V8X|1|AWTransfer RNAtransfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.35772014-07-09
346BOK|1|IASmall subunit ribosomal RNA fragment16S ribosomal RNA, mRNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.55772018-05-23
356BOK|1|LCSmall subunit ribosomal RNA fragment16S ribosomal RNA, mRNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.55772018-05-23
366BOK|1|DSmall subunit ribosomal RNA fragment16S ribosomal RNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.55772018-05-23
376BOK|1|GBSmall subunit ribosomal RNA fragment16S ribosomal RNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.55772018-05-23
383J9Z|1|S6Transfer RNAP-tRNAThermus thermophilusBacteriaRF00005Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GElectron microscopy3.6772015-07-01
395ZLU|1|DDTransfer RNAP-site tRNA, RNA (25-mer)Thermus thermophilusBacteriaRF00005Ribosome Structure bound to ABC-F protein.Electron microscopy3.6772018-08-01
403JA1|1|S2Transfer RNAmRNA, P/E-tRNAThermus thermophilusBacteriaRF00005Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GElectron microscopy3.6772015-07-01
415LMT|1|ZTransfer RNAmRNA, tRNAiThermus thermophilusBacteriaRF00005Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-3)Electron microscopy4.15772016-10-05
425LMR|1|ZTransfer RNAmRNA, tRNAiThermus thermophilusBacteriaRF00005Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)Electron microscopy4.45772016-10-05
434V68|1|AVTransfer RNAP-SITE TRNA, SYNTHETIC MRNAThermus thermophilusBacteriaRF00005T. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map.Electron microscopy6.4772014-07-09
444V5N|1|AVTransfer RNAMRNA, TRNAThermus thermophilusBacteriaRF00005tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)Electron microscopy7.6772014-07-09
454V5M|1|AVTransfer RNAMRNA, TRNAThermus thermophilusBacteriaRF00005tRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)Electron microscopy7.8772014-07-09

Release history

Release3.333.343.353.363.373.383.393.403.413.423.433.443.453.463.473.483.493.503.513.523.533.543.553.563.573.583.593.603.613.623.633.643.653.663.673.683.693.703.713.723.733.743.753.763.773.783.793.803.813.823.833.843.853.863.873.883.893.903.913.923.933.943.953.963.973.98
Date2018-08-032018-08-102018-08-172018-08-242018-08-312018-09-072018-09-142018-09-212018-09-282018-10-052018-10-122018-10-192018-10-262018-11-022018-11-092018-11-162018-11-232018-11-302018-12-072018-12-142018-12-212018-12-282019-01-042019-01-112019-01-182019-01-252019-02-012019-02-082019-02-152019-02-222019-03-012019-03-082019-03-152019-03-222019-03-292019-04-052019-04-122019-04-192019-04-262019-05-032019-05-102019-05-172019-05-242019-05-312019-06-072019-06-142019-06-212019-06-282019-07-052019-07-122019-07-192019-07-262019-08-022019-08-092019-08-162019-08-232019-08-282019-09-042019-09-112019-09-192019-09-252019-10-032019-10-092019-10-162019-10-232019-10-30

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_20.0_20721.8NR_20.0_20721.73.33(44) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 4V5M|1|AV, 4V5N|1|AV, 4V68|1|AV, 4V7J|1|Av, 4V7J|1|Aw, 4V7J|1|Bv, 4V7J|1|Bw, 4V7K|1|Av, 4V7K|1|Aw, 4V7K|1|Bv, 4V7K|1|Bw, 4V8U|1|AW, 4V8U|1|CW, 4V8X|1|AV, 4V8X|1|AW, 4V8X|1|CV, 4V8X|1|CW, 4V95|1|AV, 4V95|1|CV, 4V9A|1|AC, 4V9A|1|CC, 4V9B|1|AC, 4V9B|1|AD, 4V9B|1|CC, 4V9B|1|CD, 4V9N|1|AW, 4V9N|1|CW, 4WT8|1|C4, 5E81|1|2K, 5E81|1|2L, 5J8B|1|x, 5LMR|1|Z, 5LMT|1|Z, 6BOK|1|D, 6BOK|1|GB, 6BOK|1|IA, 6BOK|1|LC(1) 5ZLU|1|DD(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_20.0_20721.8NR_20.0_20721.93.99(44) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 4V5M|1|AV, 4V5N|1|AV, 4V68|1|AV, 4V7J|1|Av, 4V7J|1|Aw, 4V7J|1|Bv, 4V7J|1|Bw, 4V7K|1|Av, 4V7K|1|Aw, 4V7K|1|Bv, 4V7K|1|Bw, 4V8U|1|AW, 4V8U|1|CW, 4V8X|1|AV, 4V8X|1|AW, 4V8X|1|CV, 4V8X|1|CW, 4V95|1|AV, 4V95|1|CV, 4V9A|1|AC, 4V9A|1|CC, 4V9B|1|AC, 4V9B|1|AD, 4V9B|1|CC, 4V9B|1|CD, 4V9N|1|AW, 4V9N|1|CW, 4WT8|1|C4, 5E81|1|2K, 5E81|1|2L, 5J8B|1|x, 5LMR|1|Z, 5LMT|1|Z, 6BOK|1|D, 6BOK|1|GB, 6BOK|1|IA, 6BOK|1|LC(1) 5ZLU|1|DD(0)
NR_20.0_20721.8NR_20.0_29074.13.99(1) 5ZLU|1|DD(44) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 4V5M|1|AV, 4V5N|1|AV, 4V68|1|AV, 4V7J|1|Av, 4V7J|1|Aw, 4V7J|1|Bv, 4V7J|1|Bw, 4V7K|1|Av, 4V7K|1|Aw, 4V7K|1|Bv, 4V7K|1|Bw, 4V8U|1|AW, 4V8U|1|CW, 4V8X|1|AV, 4V8X|1|AW, 4V8X|1|CV, 4V8X|1|CW, 4V95|1|AV, 4V95|1|CV, 4V9A|1|AC, 4V9A|1|CC, 4V9B|1|AC, 4V9B|1|AD, 4V9B|1|CC, 4V9B|1|CD, 4V9N|1|AW, 4V9N|1|CW, 4WT8|1|C4, 5E81|1|2K, 5E81|1|2L, 5J8B|1|x, 5LMR|1|Z, 5LMT|1|Z, 6BOK|1|D, 6BOK|1|GB, 6BOK|1|IA, 6BOK|1|LC(0)

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
15ZLU|1|DDRibosome Structure bound to ABC-F protein.ELECTRON MICROSCOPY3.677
23J9Z|1|S6Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GELECTRON MICROSCOPY3.677
34V8X|1|CVStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
44V8X|1|AVStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
54V4J|1|zInteractions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.X-RAY DIFFRACTION3.8377
64V68|1|AVT. thermophilus 70S ribosome in complex with mRNA, tRNAs and EF-Tu.GDP.kirromycin ternary complex, fitted to a 6.4 A Cryo-EM map.ELECTRON MICROSCOPY6.477
74L47|1|QVCrystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-RAY DIFFRACTION3.2277
84L47|1|XVCrystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-RAY DIFFRACTION3.2277
94V95|1|AVCrystal structure of YAEJ bound to the 70S ribosomeX-RAY DIFFRACTION3.277
104V7J|1|AvStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
114V7K|1|AvStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
124V7K|1|BvStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
134V7J|1|BvStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
144V9N|1|CWCrystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-RAY DIFFRACTION3.477
154V9N|1|AWCrystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-RAY DIFFRACTION3.477
164V95|1|CVCrystal structure of YAEJ bound to the 70S ribosomeX-RAY DIFFRACTION3.277
174WT8|1|C4Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complexX-RAY DIFFRACTION3.477
184V9A|1|CCCrystal Structure of the 70S ribosome with tetracycline.X-RAY DIFFRACTION3.377
194V9B|1|CCCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
204V9A|1|ACCrystal Structure of the 70S ribosome with tetracycline.X-RAY DIFFRACTION3.377
214V9B|1|ACCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
225E81|1|2KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9577
235J8B|1|xCrystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosomeX-RAY DIFFRACTION2.677
246BOK|1|IAE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5577
256BOK|1|LCE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5577
265E81|1|2LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9577
275LMR|1|ZStructure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B)ELECTRON MICROSCOPY4.4577
285LMT|1|ZStructure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-3)ELECTRON MICROSCOPY4.1577
294V5N|1|AVtRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST)ELECTRON MICROSCOPY7.677
304V8U|1|CWCrystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-RAY DIFFRACTION3.777
314V8U|1|AWCrystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-RAY DIFFRACTION3.777
324V5A|1|AWStructure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-RAY DIFFRACTION3.577
334V5A|1|CWStructure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-RAY DIFFRACTION3.577
344V7K|1|BwStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
354V7J|1|BwStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
364V8X|1|CWStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
374V7J|1|AwStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
384V8X|1|AWStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
394V7K|1|AwStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
406BOK|1|DE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5577
416BOK|1|GBE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5577
424V9B|1|ADCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
434V9B|1|CDCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
444V5M|1|AVtRNA tranlocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE)ELECTRON MICROSCOPY7.877
453JA1|1|S2Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GELECTRON MICROSCOPY3.677

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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