RNA 3D Hub //

Equivalence class NR_4.0_20721.8 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
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 diffraction2.952016-01-27
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 diffraction2.62016-05-25
34V95|1|AVTransfer RNAmRNA, P-site fMet-tRNAThermus thermophilusBacteriaRF00005Crystal structure of YAEJ bound to the 70S ribosomeX-ray diffraction3.22014-07-09
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 diffraction3.32014-07-09
54V9B|1|ACTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.12014-07-09
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 diffraction3.32014-07-09
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 diffraction2.952016-01-27
84V9B|1|CCTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.12014-07-09
94V95|1|CVTransfer RNAmRNA, P-site fMet-tRNAThermus thermophilusBacteriaRF00005Crystal structure of YAEJ bound to the 70S ribosomeX-ray diffraction3.22014-07-09
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 diffraction3.62014-07-09
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 diffraction3.62014-07-09
124WT8|1|C4Transfer RNAmRNA, P site trNAThermus thermophilusBacteriaRF00005Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complexX-ray diffraction3.42015-01-21
134V9A|1|ACTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tetracycline.X-ray diffraction3.32014-07-09
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 diffraction3.222014-08-06
154V7K|1|BwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.62014-07-09
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 diffraction3.222014-08-06
174V7K|1|AwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-ray diffraction3.62014-07-09
184V9A|1|CCTransfer RNAMRNA, TRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tetracycline.X-ray diffraction3.32014-07-09
194V7J|1|AwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.32014-07-09
204V7J|1|BwTransfer RNARNA (77-MER)Thermus thermophilusBacteriaRF00005Structure of RelE nuclease bound to the 70S ribosome (precleavage state)X-ray diffraction3.32014-07-09
214V9B|1|CDTransfer RNATRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.12014-07-09
224V4J|1|zTransfer RNAMRNA, P-site tRNAfMETThermus thermophilusBacteriaRF00005Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.X-ray diffraction3.832014-07-09
234V9B|1|ADTransfer RNATRNA-FMETThermus thermophilusBacteriaRF00005Crystal Structure of the 70S ribosome with tigecycline.X-ray diffraction3.12014-07-09
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 diffraction3.52014-07-09
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 diffraction3.52014-07-09
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 diffraction3.352014-07-09
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 diffraction3.42014-07-09
284V8X|1|CVTransfer RNABACTERIAL TOXIN YOEB, transfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.352014-07-09
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 diffraction3.42014-07-09
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 diffraction3.72014-07-09
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 diffraction3.72014-07-09
324V8X|1|CWTransfer RNAtransfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.352014-07-09
334V8X|1|AWTransfer RNAtransfer RNAThermus thermophilusBacteriaRF00005Structure of Thermus thermophilus ribosomeX-ray diffraction3.352014-07-09
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 diffraction3.552018-05-23
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 diffraction3.552018-05-23
366BOK|1|DSmall subunit ribosomal RNA fragment16S ribosomal RNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.552018-05-23
376BOK|1|GBSmall subunit ribosomal RNA fragment16S ribosomal RNAThermus thermophilusBacteriaRF00005E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-ray diffraction3.552018-05-23
383J9Z|1|S6Transfer RNAP-tRNAThermus thermophilusBacteriaRF00005Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GElectron microscopy3.62015-07-01
395ZLU|1|DDTransfer RNAP-site tRNA, RNA (25-mer)Thermus thermophilusBacteriaRF00005Ribosome Structure bound to ABC-F protein.Electron microscopy3.62018-08-01
403JA1|1|S2Transfer RNAmRNA, P/E-tRNAThermus thermophilusBacteriaRF00005Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GElectron microscopy3.62015-07-01

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_4.0_20721.8NR_4.0_20721.73.33(39) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 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, 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_4.0_20721.8NR_4.0_20721.93.99(39) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 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, 6BOK|1|D, 6BOK|1|GB, 6BOK|1|IA, 6BOK|1|LC(1) 5ZLU|1|DD(0)
NR_4.0_20721.8NR_4.0_29074.13.99(1) 5ZLU|1|DD(39) 3J9Z|1|S6, 3JA1|1|S2, 4L47|1|QV, 4L47|1|XV, 4V4J|1|z, 4V5A|1|AW, 4V5A|1|CW, 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, 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.

#SViewPDBTitleMethodResolutionLength
15ZLU|1|DDRibosome Structure bound to ABC-F protein.ELECTRON MICROSCOPY3.672
23J9Z|1|S6Activation of GTP Hydrolysis in mRNA-tRNA Translocation by Elongation Factor GELECTRON MICROSCOPY3.677
35E81|1|2LStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9572
46BOK|1|LCE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5573
56BOK|1|IAE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5573
65J8B|1|xCrystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosomeX-RAY DIFFRACTION2.673
75E81|1|2KStructure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pairX-RAY DIFFRACTION2.9572
84V9B|1|ACCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
94V9A|1|ACCrystal Structure of the 70S ribosome with tetracycline.X-RAY DIFFRACTION3.377
104V9B|1|CCCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
114V9A|1|CCCrystal Structure of the 70S ribosome with tetracycline.X-RAY DIFFRACTION3.377
124WT8|1|C4Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complexX-RAY DIFFRACTION3.477
134L47|1|QVCrystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-RAY DIFFRACTION3.2277
144L47|1|XVCrystal Structure of Frameshift Suppressor tRNA SufA6 Bound to Codon CCC-U on the RibosomeX-RAY DIFFRACTION3.2277
154V95|1|AVCrystal structure of YAEJ bound to the 70S ribosomeX-RAY DIFFRACTION3.277
164V9N|1|AWCrystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-RAY DIFFRACTION3.477
174V9N|1|CWCrystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.X-RAY DIFFRACTION3.477
184V7K|1|BvStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.676
194V7J|1|BvStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.376
204V7J|1|AvStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.376
214V7K|1|AvStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.676
224V95|1|CVCrystal structure of YAEJ bound to the 70S ribosomeX-RAY DIFFRACTION3.277
234V4J|1|zInteractions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.X-RAY DIFFRACTION3.8377
244V8X|1|CVStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
254V8X|1|AVStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3576
264V8U|1|CWCrystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-RAY DIFFRACTION3.776
274V8U|1|AWCrystal Structure of 70S Ribosome with Both Cognate tRNAs in the E and P Sites Representing an Authentic Elongation Complex.X-RAY DIFFRACTION3.776
284V5A|1|AWStructure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-RAY DIFFRACTION3.576
294V5A|1|CWStructure of the Ribosome Recycling Factor bound to the Thermus thermophilus 70S ribosome with mRNA, ASL-Phe and tRNA-fMetX-RAY DIFFRACTION3.576
304V7K|1|AwStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
314V8X|1|AWStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
324V7J|1|AwStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
334V8X|1|CWStructure of Thermus thermophilus ribosomeX-RAY DIFFRACTION3.3577
344V7J|1|BwStructure of RelE nuclease bound to the 70S ribosome (precleavage state)X-RAY DIFFRACTION3.377
354V7K|1|BwStructure of RelE nuclease bound to the 70S ribosome (postcleavage state)X-RAY DIFFRACTION3.677
366BOK|1|DE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5573
376BOK|1|GBE. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosomeX-RAY DIFFRACTION3.5573
384V9B|1|CDCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
394V9B|1|ADCrystal Structure of the 70S ribosome with tigecycline.X-RAY DIFFRACTION3.177
403JA1|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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