RNA 3D Hub //

Equivalence class NR_3.0_83717.59 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
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 diffraction328972016-07-27
24YBB|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High-resolution structure of the Escherichia coli ribosomeX-ray diffraction2.128972015-03-18
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 diffraction328972015-08-05
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 diffraction328972015-08-05
56I7V|1|DALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Ribosomal protein paralogs bL31 and bL36X-ray diffraction2.928972018-12-05
65J91|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the Wild-type 70S E coli ribosome bound to TigecyclineX-ray diffraction2.9628972016-07-06
74V9P|1|EALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
84V9P|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
94V9P|1|GALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
104V9P|1|AALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
114V9D|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-ray diffraction328972014-07-09
124V9O|1|AALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
134V9O|1|EALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
144V9O|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
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 diffraction328982016-07-27
164U27|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin and linopristin.X-ray diffraction2.828972014-07-30
174U24|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin.X-ray diffraction2.928972014-07-30
184U25|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to virginiamycin M1.X-ray diffraction2.928972014-07-30
194V9D|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structures of the bacterial ribosome in classical and hybrid states of tRNA bindingX-ray diffraction328962014-07-09
204U26|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-ray diffraction2.828972014-07-30
214V9O|1|GALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Control of ribosomal subunit rotation by elongation factor GX-ray diffraction2.928542014-07-09
224U1U|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to quinupristin.X-ray diffraction2.9528972014-07-30
234YBB|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High-resolution structure of the Escherichia coli ribosomeX-ray diffraction2.128982015-03-18
244U1V|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to linopristin.X-ray diffraction328972014-07-30
254U20|1|BALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin.X-ray diffraction2.928972014-07-30
266I7V|1|CALarge subunit ribosomal RNA23S ribsomal RNAEscherichia coliBacteriaRF02541Ribosomal protein paralogs bL31 and bL36X-ray diffraction2.928982018-12-05
274U27|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin and linopristin.X-ray diffraction2.828972014-07-30
284U25|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to virginiamycin M1.X-ray diffraction2.928972014-07-30
294U1U|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to quinupristin.X-ray diffraction2.9528972014-07-30
304U1V|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to linopristin.X-ray diffraction328972014-07-30
314U24|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin.X-ray diffraction2.928972014-07-30
324U26|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-ray diffraction2.828972014-07-30
334U20|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Crystal structure of the E. coli ribosome bound to flopristin.X-ray diffraction2.928972014-07-30
345J91|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the Wild-type 70S E coli ribosome bound to TigecyclineX-ray diffraction2.9628982016-07-06
355J5B|1|DALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the WT E coli ribosome bound to tetracyclineX-ray diffraction2.828972016-07-27
365J5B|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Structure of the WT E coli ribosome bound to tetracyclineX-ray diffraction2.828982016-07-27
376HRM|1|1Small subunit ribosomal RNAstapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNA,stapled 16S-23S rRNAEscherichia coliBacteriaRF02541E. coli 70S d2d8 stapled ribosomeElectron microscopy2.9644502018-12-19
386PJ6|1|ILarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541High resolution cryo-EM structure of E.coli 50SElectron microscopy2.228982020-01-22
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 microscopy2.728972020-01-01
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 microscopy2.728972020-01-01
416QDW|1|bLarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541Cryo-EM structure of the 50S ribosomal subunit at 2.83 Angstroms with modeled GBC SecM peptideElectron microscopy2.8328882020-01-15
425AFI|1|ALarge subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF025412.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EMElectron microscopy2.929002015-03-11
436U48|1|CALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF02541E. coli 50S with phazolicin (PHZ) bound in exit tunnelElectron microscopy2.8728982019-09-18
445NWY|1|NLarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF025412.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complexElectron microscopy2.928972017-07-19
456ORE|1|1Large subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Release complex 70SElectron microscopy2.929032019-06-19
465MDV|1|1Large subunit ribosomal RNA23S ribosomal RNAEscherichia coliBacteriaRF02541Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)Electron microscopy2.9729032016-12-14
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 microscopy329002018-09-05
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 microscopy327952019-04-10
495WFS|1|ALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF0254170S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)Electron microscopy329002018-05-02
505WDT|1|ALarge subunit ribosomal RNA23S rRNAEscherichia coliBacteriaRF0254170S ribosome-EF-Tu H84A complex with GppNHpElectron microscopy329002018-04-25
515IQR|1|1Large subunit ribosomal RNALSU rRNAEscherichia coliBacteriaRF02541Structure of RelA bound to the 70S ribosomeElectron microscopy329042016-05-04

Release history

Release3.1293.130
Date2020-06-032020-06-10

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_3.0_83717.59NR_3.0_83717.583.129(51) 4U1U|1|BA, 4U1U|1|DA, 4U1V|1|BA, 4U1V|1|DA, 4U20|1|BA, 4U20|1|DA, 4U24|1|BA, 4U24|1|DA, 4U25|1|BA, 4U25|1|DA, 4U26|1|BA, 4U26|1|DA, 4U27|1|BA, 4U27|1|DA, 4V9D|1|CA, 4V9D|1|DA, 4V9O|1|AA, 4V9O|1|CA, 4V9O|1|EA, 4V9O|1|GA, 4V9P|1|AA, 4V9P|1|CA, 4V9P|1|EA, 4V9P|1|GA, 4WOI|1|BA, 4WOI|1|CA, 4YBB|1|CA, 4YBB|1|DA, 5AFI|1|A, 5IQR|1|1, 5J5B|1|CA, 5J5B|1|DA, 5J7L|1|CA, 5J7L|1|DA, 5J91|1|CA, 5J91|1|DA, 5MDV|1|1, 5NWY|1|N, 5WDT|1|A, 5WFS|1|A, 6H4N|1|A, 6HRM|1|1, 6I7V|1|CA, 6I7V|1|DA, 6ORE|1|1, 6PJ6|1|I, 6QDW|1|b, 6QUL|1|A, 6TBV|1|23S1, 6TC3|1|23S1, 6U48|1|CA(0) (0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_3.0_83717.59NR_3.0_83717.603.131(51) 4U1U|1|BA, 4U1U|1|DA, 4U1V|1|BA, 4U1V|1|DA, 4U20|1|BA, 4U20|1|DA, 4U24|1|BA, 4U24|1|DA, 4U25|1|BA, 4U25|1|DA, 4U26|1|BA, 4U26|1|DA, 4U27|1|BA, 4U27|1|DA, 4V9D|1|CA, 4V9D|1|DA, 4V9O|1|AA, 4V9O|1|CA, 4V9O|1|EA, 4V9O|1|GA, 4V9P|1|AA, 4V9P|1|CA, 4V9P|1|EA, 4V9P|1|GA, 4WOI|1|BA, 4WOI|1|CA, 4YBB|1|CA, 4YBB|1|DA, 5AFI|1|A, 5IQR|1|1, 5J5B|1|CA, 5J5B|1|DA, 5J7L|1|CA, 5J7L|1|DA, 5J91|1|CA, 5J91|1|DA, 5MDV|1|1, 5NWY|1|N, 5WDT|1|A, 5WFS|1|A, 6H4N|1|A, 6HRM|1|1, 6I7V|1|CA, 6I7V|1|DA, 6ORE|1|1, 6PJ6|1|I, 6QDW|1|b, 6QUL|1|A, 6TBV|1|23S1, 6TC3|1|23S1, 6U48|1|CA(0) (10) 6PC5|1|I, 6PC6|1|I, 6PC7|1|I, 6PC8|1|I, 6PCH|1|I, 6PCQ|1|I, 6PCR|1|I, 6PCS|1|I, 6PCT|1|I, 6WYV|1|I

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
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
54U25|1|BACrystal structure of the E. coli ribosome bound to virginiamycin M1.X-RAY DIFFRACTION2.92897
64U27|1|BACrystal structure of the E. coli ribosome bound to flopristin and linopristin.X-RAY DIFFRACTION2.82897
74U1V|1|BACrystal structure of the E. coli ribosome bound to linopristin.X-RAY DIFFRACTION32897
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 MICROSCOPY32904
115AFI|1|A2.9A Structure of E. coli ribosome-EF-TU complex by cs-corrected cryo-EMELECTRON MICROSCOPY2.92900
126H4N|1|AStructure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli RibosomeELECTRON MICROSCOPY32900
135WFS|1|A70S ribosome-EF-Tu H84A complex with GTP and near-cognate tRNA (Complex C4)ELECTRON MICROSCOPY32900
145WDT|1|A70S ribosome-EF-Tu H84A complex with GppNHpELECTRON MICROSCOPY32900
156TBV|1|23S1Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 2)ELECTRON MICROSCOPY2.72897
166TC3|1|23S1Cryo-EM structure of an Escherichia coli ribosome-SpeFL complex stalled in response to L-ornithine (Replicate 1)ELECTRON MICROSCOPY2.72897
176ORE|1|1Release complex 70SELECTRON MICROSCOPY2.92903
185MDV|1|1Structure of ArfA and RF2 bound to the 70S ribosome (accommodated state)ELECTRON MICROSCOPY2.972903
195NWY|1|N2.9 A cryo-EM structure of VemP-stalled ribosome-nascent chain complexELECTRON MICROSCOPY2.92897
206QUL|1|AStructure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolidELECTRON MICROSCOPY32795
214YBB|1|DAHigh-resolution structure of the Escherichia coli ribosomeX-RAY DIFFRACTION2.12897
225J5B|1|DAStructure of the WT E coli ribosome bound to tetracyclineX-RAY DIFFRACTION2.82897
235J91|1|DAStructure of the Wild-type 70S E coli ribosome bound to TigecyclineX-RAY DIFFRACTION2.962897
245J7L|1|DAStructure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-RAY DIFFRACTION32897
256I7V|1|DARibosomal protein paralogs bL31 and bL36X-RAY DIFFRACTION2.92897
266PJ6|1|IHigh resolution cryo-EM structure of E.coli 50SELECTRON MICROSCOPY2.22898
276U48|1|CAE. coli 50S with phazolicin (PHZ) bound in exit tunnelELECTRON MICROSCOPY2.872898
285J7L|1|CAStructure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracyclineX-RAY DIFFRACTION32898
295J5B|1|CAStructure of the WT E coli ribosome bound to tetracyclineX-RAY DIFFRACTION2.82898
305J91|1|CAStructure of the Wild-type 70S E coli ribosome bound to TigecyclineX-RAY DIFFRACTION2.962898
314YBB|1|CAHigh-resolution structure of the Escherichia coli ribosomeX-RAY DIFFRACTION2.12898
326I7V|1|CARibosomal protein paralogs bL31 and bL36X-RAY DIFFRACTION2.92898
334U26|1|DACrystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.X-RAY DIFFRACTION2.82897
344U24|1|DACrystal structure of the E. coli ribosome bound to dalfopristin.X-RAY DIFFRACTION2.92897
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 MICROSCOPY2.964450

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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