RNA 3D Hub //

Equivalence class NR_3.0_83717.57 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
15J7L|1|DA (rep)Large subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-ray diffraction32016-07-27
24YBB|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High-resolution structure of the Escherichia coli ribosomeX-ray diffraction2.12015-03-18
34WOI|1|BALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF025414,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2X-ray diffraction32015-08-05
44WOI|1|CALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF025414,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2X-ray diffraction32015-08-05
56I7V|1|DALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Ribosomal protein paralogs bL31 and bL36X-ray diffraction2.92018-12-05
65J91|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the Wild-type 70S E coli ribosome bound to TigecyclineX-ray diffraction2.962016-07-06
74V9P|1|EALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
84V9P|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
94V9P|1|GALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
104V9P|1|AALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
114V9D|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-ray diffraction32014-07-09
124V9O|1|AALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
134V9O|1|EALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
144V9O|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
155J7L|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-ray diffraction32016-07-27
164U27|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin and linopristin.X-ray diffraction2.82014-07-30
174U24|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin.X-ray diffraction2.92014-07-30
184U25|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to virginiamycin M1.X-ray diffraction2.92014-07-30
194V9D|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-ray diffraction32014-07-09
204U26|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-ray diffraction2.82014-07-30
214V9O|1|GALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.92014-07-09
224U1U|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to quinupristin.X-ray diffraction2.952014-07-30
234YBB|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High-resolution structure of the Escherichia coli ribosomeX-ray diffraction2.12015-03-18
244U1V|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to linopristin.X-ray diffraction32014-07-30
254U20|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin.X-ray diffraction2.92014-07-30
266I7V|1|CALarge subunit ribosomal RNA23S ribsomal RNAEscherichia coliBacteriaRF02541Ribosomal protein paralogs bL31 and bL36X-ray diffraction2.92018-12-05
274U27|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin and linopristin.X-ray diffraction2.82014-07-30
284U25|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to virginiamycin M1.X-ray diffraction2.92014-07-30
294U1U|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to quinupristin.X-ray diffraction2.952014-07-30
304U1V|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to linopristin.X-ray diffraction32014-07-30
314U24|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin.X-ray diffraction2.92014-07-30
324U26|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-ray diffraction2.82014-07-30
334U20|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin.X-ray diffraction2.92014-07-30
345J91|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the Wild-type 70S E coli ribosome bound to TigecyclineX-ray diffraction2.962016-07-06
355J5B|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the WT E coli ribosome bound to tetracyclineX-ray diffraction2.82016-07-27
365J5B|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the WT E coli ribosome bound to tetracyclineX-ray diffraction2.82016-07-27
376HRM|1|1Small subunit ribosomal RNAstapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNAEscherichia coliBacteriaRF00177E. coli 70S d2d8 stapled ribosomeElectron microscopy2.962018-12-19
386PJ6|1|ILarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High resolution cryo-EM structure of E.coli 50SElectron microscopy2.22020-01-22
396TBV|1|23S1Large subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 2)Electron microscopy2.72020-01-01
406TC3|1|23S1Large subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)Electron microscopy2.72020-01-01
416QDW|1|bLarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptideElectron microscopy2.832020-01-15
425AFI|1|ALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF025412.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EMElectron microscopy2.92015-03-11
436U48|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541E. coli 50S with phazolicin (PHZ) bound in exit tunnelElectron microscopy2.872019-09-18
445NWY|1|NLarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF025412.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complexElectron microscopy2.92017-07-19
456ORE|1|1Large subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Release complex 70SElectron microscopy2.92019-06-19
465MDV|1|1Large subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)Electron microscopy2.972016-12-14
476H4N|1|ALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli RibosomeElectron microscopy32018-09-05
486QUL|1|ALarge subunit ribosomal RNA23S rRNA, P-site fMet-tRNA(fMet)Escherichia coliBacteriaRF02541Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolidElectron microscopy32019-04-10
495WFS|1|ALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF0254170S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)Electron microscopy32018-05-02
505WDT|1|ALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF0254170S ribosome-EF-Tu H84A complex with GppNHpElectron microscopy32018-04-25
515IQR|1|1Large subunit ribosomal RNALSU rRNAEscherichia coliBacteriaRF02541Structure of RelA bound to the 70S ribosomeElectron microscopy32016-05-04

Release history

Release3.1103.1113.1123.1133.1143.1153.1163.1173.1183.1193.1203.1213.1223.1233.124
Date2020-01-222020-01-292020-02-052020-02-122020-02-192020-02-262020-03-042020-03-112020-03-182020-03-252020-04-012020-04-082020-04-152020-04-222020-04-29

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_3.0_83717.57NR_3.0_83717.563.110(50) 6H4N|1|A, 4U25|1|BA, 4U24|1|DA, 5WFS|1|A, 4U24|1|BA, 5WDT|1|A, 4U20|1|DA, 5NWY|1|N, 4U20|1|BA, 5MDV|1|1, 4U1V|1|DA, 5J91|1|DA, 4U1V|1|BA, 5J91|1|CA, 4U1U|1|DA, 5J7L|1|DA, 4U1U|1|BA, 5J7L|1|CA, 5J5B|1|DA, 5J5B|1|CA, 5IQR|1|1, 5AFI|1|A, 4YBB|1|DA, 4YBB|1|CA, 4WOI|1|CA, 4WOI|1|BA, 4V9P|1|GA, 4V9P|1|EA, 4V9P|1|CA, 4V9P|1|AA, 4V9O|1|GA, 4V9O|1|EA, 6U48|1|CA, 4V9O|1|CA, 6TC3|1|23S1, 4V9O|1|AA, 6TBV|1|23S1, 4V9D|1|DA, 6QUL|1|A, 4V9D|1|CA, 6QDW|1|b, 4U27|1|DA, 6ORE|1|1, 4U27|1|BA, 6I7V|1|DA, 4U26|1|DA, 6I7V|1|CA, 4U26|1|BA, 6HRM|1|1, 4U25|1|DA(1) 6PJ6|1|I(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_3.0_83717.57NR_3.0_83717.583.125(51) 6U48|1|CA, 5MDV|1|1, 5J91|1|DA, 5J91|1|CA, 5J7L|1|DA, 5J7L|1|CA, 5J5B|1|DA, 5J5B|1|CA, 5IQR|1|1, 5AFI|1|A, 4YBB|1|DA, 5NWY|1|N, 5WDT|1|A, 5WFS|1|A, 6TC3|1|23S1, 6TBV|1|23S1, 6QUL|1|A, 6QDW|1|b, 6PJ6|1|I, 6ORE|1|1, 6I7V|1|DA, 6I7V|1|CA, 6HRM|1|1, 6H4N|1|A, 4YBB|1|CA, 4WOI|1|CA, 4WOI|1|BA, 4U26|1|BA, 4U25|1|DA, 4U25|1|BA, 4U24|1|DA, 4U24|1|BA, 4U20|1|DA, 4U20|1|BA, 4U1V|1|DA, 4U1V|1|BA, 4U1U|1|DA, 4U26|1|DA, 4U27|1|BA, 4U27|1|DA, 4V9P|1|GA, 4V9P|1|EA, 4V9P|1|CA, 4V9P|1|AA, 4V9O|1|GA, 4V9O|1|EA, 4V9O|1|CA, 4V9O|1|AA, 4V9D|1|DA, 4V9D|1|CA, 4U1U|1|BA(0) (0)

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5

#S - ordering by similarity (same as in the heat map).
#SPDBTitleMethodResolutionLength
14WOI|1|BA4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2X-RAY DIFFRACTION32897
24V9D|1|CAStructures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-RAY DIFFRACTION32897
34U1U|1|BACrystal structure of the E. coli ribosome bound to quinupristin.X-RAY DIFFRACTION2.952897
44U20|1|BACrystal structure of the E. coli ribosome bound to flopristin.X-RAY DIFFRACTION2.92897
54U1V|1|BACrystal structure of the E. coli ribosome bound to linopristin.X-RAY DIFFRACTION32897
64U27|1|BACrystal structure of the E. coli ribosome bound to flopristin and linopristin.X-RAY DIFFRACTION2.82897
74U25|1|BACrystal structure of the E. coli ribosome bound to virginiamycin M1.X-RAY DIFFRACTION2.92897
84U26|1|BACrystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-RAY DIFFRACTION2.82897
94U24|1|BACrystal structure of the E. coli ribosome bound to dalfopristin.X-RAY DIFFRACTION2.92897
105IQR|1|1Structure of RelA bound to the 70S ribosomeELECTRON MICROSCOPY32882
116H4N|1|AStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli RibosomeELECTRON MICROSCOPY32900
125AFI|1|A2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EMELECTRON MICROSCOPY2.92876
135WFS|1|A70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)ELECTRON MICROSCOPY32876
145WDT|1|A70S ribosome-EF-Tu H84A complex with GppNHpELECTRON MICROSCOPY32876
155NWY|1|N2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complexELECTRON MICROSCOPY2.92898
165MDV|1|1Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)ELECTRON MICROSCOPY2.972881
176ORE|1|1Release complex 70SELECTRON MICROSCOPY2.92881
186TC3|1|23S1Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)ELECTRON MICROSCOPY2.72874
196TBV|1|23S1Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 2)ELECTRON MICROSCOPY2.72874
206QUL|1|AStructure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolidELECTRON MICROSCOPY32799
215J7L|1|DAStructure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-RAY DIFFRACTION32886
225J91|1|DAStructure of the Wild-type 70S E coli ribosome bound to TigecyclineX-RAY DIFFRACTION2.962886
235J5B|1|DAStructure of the WT E coli ribosome bound to tetracyclineX-RAY DIFFRACTION2.82886
244YBB|1|DAHigh-resolution structure of the Escherichia coli ribosomeX-RAY DIFFRACTION2.12883
256I7V|1|DARibosomal protein paralogs bL31 and bL36X-RAY DIFFRACTION2.92875
266PJ6|1|IHigh resolution cryo-EM structure of E.coli 50SELECTRON MICROSCOPY2.22874
276U48|1|CAE. coli 50S with phazolicin (PHZ) bound in exit tunnelELECTRON MICROSCOPY2.872875
285J7L|1|CAStructure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-RAY DIFFRACTION32875
295J91|1|CAStructure of the Wild-type 70S E coli ribosome bound to TigecyclineX-RAY DIFFRACTION2.962876
305J5B|1|CAStructure of the WT E coli ribosome bound to tetracyclineX-RAY DIFFRACTION2.82876
314YBB|1|CAHigh-resolution structure of the Escherichia coli ribosomeX-RAY DIFFRACTION2.12876
326I7V|1|CARibosomal protein paralogs bL31 and bL36X-RAY DIFFRACTION2.92898
334U24|1|DACrystal structure of the E. coli ribosome bound to dalfopristin.X-RAY DIFFRACTION2.92897
344U26|1|DACrystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-RAY DIFFRACTION2.82897
354U25|1|DACrystal structure of the E. coli ribosome bound to virginiamycin M1.X-RAY DIFFRACTION2.92897
364U27|1|DACrystal structure of the E. coli ribosome bound to flopristin and linopristin.X-RAY DIFFRACTION2.82897
374U1V|1|DACrystal structure of the E. coli ribosome bound to linopristin.X-RAY DIFFRACTION32897
384U20|1|DACrystal structure of the E. coli ribosome bound to flopristin.X-RAY DIFFRACTION2.92897
394U1U|1|DACrystal structure of the E. coli ribosome bound to quinupristin.X-RAY DIFFRACTION2.952897
404V9D|1|DAStructures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-RAY DIFFRACTION32896
414WOI|1|CA4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2X-RAY DIFFRACTION32897
424V9P|1|GAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
434V9O|1|GAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
444V9O|1|EAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
454V9P|1|EAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
464V9P|1|AAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
474V9O|1|AAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
484V9P|1|CAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
494V9O|1|CAControl of ribosomal subunit rotation by elongation factor GX-RAY DIFFRACTION2.92854
506QDW|1|bCryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptideELECTRON MICROSCOPY2.832888
516HRM|1|1E. coli 70S d2d8 stapled ribosomeELECTRON MICROSCOPY2.964417
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