RNA 3D Hub //

Equivalence class NR_2.0_10157.151 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18B0X|1|b (rep)5S ribosomal RNA5S rRNAEscherichia coli BBacteriaRF00001Translating 70S ribosome in the unrotated state (P and E, tRNAs)Electron microscopy1.551192022-11-30
28CEU|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Retapamulin and Capreomycin bound to the 50S subunitElectron microscopy1.831192023-07-26
38FTO|1|b5S ribosomal RNA5S rRNAEscherichia coliBacteriaRF00001E. coli 70S ribosome with an improved MS2 tag inserted in H98Electron microscopy1.851192023-08-02
49GHE|1|b5S ribosomal RNA5S rRNAEscherichia coli K-12BacteriaRF00001Staphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S ribosome (FusB-70S:SSU)Electron microscopy1.871192025-03-26
59D89|1|E5S ribosomal RNA5S rRNAEscherichia coliBacteriaRF00001E. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)Electron microscopy1.951192025-01-22
68AYE|1|b5S ribosomal RNA5S rRNAEscherichia coliBacteriaRF00001E. coli 70S ribosome bound to thermorubin and fMet-tRNAElectron microscopy1.961192023-03-01
77K00|1|b5S ribosomal RNA5S rRNAEscherichia coliBacteriaRF00001Structure of the Bacterial Ribosome at 2 Angstrom ResolutionElectron microscopy1.981192020-09-23
88CGD|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Clindamycin bound to the 50S subunitElectron microscopy1.981192023-07-26
98QOA|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Structure of SecM-stalled Escherichia coli 70S ribosomeElectron microscopy21192024-03-20
108E30|1|J5S ribosomal RNA5S ribosomal RNAEscherichia coliBacteriaRF00001E. coli 50S ribosome bound to compound streptogramin A analog 3142Electron microscopy1.911182023-06-28
118E3O|1|J5S ribosomal RNA5S ribosomal RNAEscherichia coliBacteriaRF00001E. coli 50S ribosome bound to solithromycin and VM1Electron microscopy1.991182023-06-28
128CGV|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Tiamulin bound to the 50S subunitElectron microscopy1.66562023-08-02
138CGK|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Lincomycin and Avilamycin bound to the 50S subunitElectron microscopy1.64392023-07-19
148CAM|1|b5S ribosomal RNA5S rRNAEscherichia coli BW25113BacteriaRF00001Evernimicin bound to the 50S subunitElectron microscopy1.86342023-07-26

Release history

Release3.3813.3823.3833.3843.3853.386
Date2025-04-022025-04-092025-04-162025-04-232025-04-302025-05-07

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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
19D89|1|EE. coli 50S ribosomal subunit in complex with PrAMP rumicidin-2 (focused refinement)ELECTRON MICROSCOPY1.95119
28QOA|1|bStructure of SecM-stalled Escherichia coli 70S ribosomeELECTRON MICROSCOPY2119
38B0X|1|bTranslating 70S ribosome in the unrotated state (P and E, tRNAs)ELECTRON MICROSCOPY1.55119
47K00|1|bStructure of the Bacterial Ribosome at 2 Angstrom ResolutionELECTRON MICROSCOPY1.98119
58FTO|1|bE. coli 70S ribosome with an improved MS2 tag inserted in H98ELECTRON MICROSCOPY1.85119
69GHE|1|bStaphylococcus aureus FusB bound to the small subunit of the Escherichia coli 70S ribosome (FusB-70S:SSU)ELECTRON MICROSCOPY1.87119
78AYE|1|bE. coli 70S ribosome bound to thermorubin and fMet-tRNAELECTRON MICROSCOPY1.96119
88CGV|1|bTiamulin bound to the 50S subunitELECTRON MICROSCOPY1.6656
98CEU|1|bRetapamulin and Capreomycin bound to the 50S subunitELECTRON MICROSCOPY1.83119
108CGD|1|bClindamycin bound to the 50S subunitELECTRON MICROSCOPY1.98119
118CAM|1|bEvernimicin bound to the 50S subunitELECTRON MICROSCOPY1.8634
128CGK|1|bLincomycin and Avilamycin bound to the 50S subunitELECTRON MICROSCOPY1.6439
138E30|1|JE. coli 50S ribosome bound to compound streptogramin A analog 3142ELECTRON MICROSCOPY1.91118
148E3O|1|JE. coli 50S ribosome bound to solithromycin and VM1ELECTRON MICROSCOPY1.99118

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.

9D89|1|E:9D89|1|E = 09D89|1|E:8QOA|1|b = 0.07079D89|1|E:8B0X|1|b = 0.06439D89|1|E:7K00|1|b = 0.06059D89|1|E:8FTO|1|b = 0.06759D89|1|E:9GHE|1|b = 0.06609D89|1|E:8AYE|1|b = 0.06519D89|1|E:8CGV|1|b = 0.08659D89|1|E:8CEU|1|b = 0.06499D89|1|E:8CGD|1|b = 0.07259D89|1|E:8CAM|1|b = 0.07529D89|1|E:8CGK|1|b = 0.08499D89|1|E:8E30|1|J = 0.07129D89|1|E:8E3O|1|J = 0.07738QOA|1|b:9D89|1|E = 0.07078QOA|1|b:8QOA|1|b = 08QOA|1|b:8B0X|1|b = 0.04398QOA|1|b:7K00|1|b = 0.04438QOA|1|b:8FTO|1|b = 0.04968QOA|1|b:9GHE|1|b = 0.04368QOA|1|b:8AYE|1|b = 0.04198QOA|1|b:8CGV|1|b = 0.06468QOA|1|b:8CEU|1|b = 0.05108QOA|1|b:8CGD|1|b = 0.05858QOA|1|b:8CAM|1|b = 0.08828QOA|1|b:8CGK|1|b = 0.10878QOA|1|b:8E30|1|J = 0.06468QOA|1|b:8E3O|1|J = 0.07228B0X|1|b:9D89|1|E = 0.06438B0X|1|b:8QOA|1|b = 0.04398B0X|1|b:8B0X|1|b = 08B0X|1|b:7K00|1|b = 0.03598B0X|1|b:8FTO|1|b = 0.04158B0X|1|b:9GHE|1|b = 0.03318B0X|1|b:8AYE|1|b = 0.03118B0X|1|b:8CGV|1|b = 0.03928B0X|1|b:8CEU|1|b = 0.04998B0X|1|b:8CGD|1|b = 0.06048B0X|1|b:8CAM|1|b = 0.08218B0X|1|b:8CGK|1|b = 0.06998B0X|1|b:8E30|1|J = 0.06038B0X|1|b:8E3O|1|J = 0.07147K00|1|b:9D89|1|E = 0.06057K00|1|b:8QOA|1|b = 0.04437K00|1|b:8B0X|1|b = 0.03597K00|1|b:7K00|1|b = 07K00|1|b:8FTO|1|b = 0.03157K00|1|b:9GHE|1|b = 0.03007K00|1|b:8AYE|1|b = 0.02617K00|1|b:8CGV|1|b = 0.04197K00|1|b:8CEU|1|b = 0.03737K00|1|b:8CGD|1|b = 0.04527K00|1|b:8CAM|1|b = 0.07557K00|1|b:8CGK|1|b = 0.06797K00|1|b:8E30|1|J = 0.05717K00|1|b:8E3O|1|J = 0.06648FTO|1|b:9D89|1|E = 0.06758FTO|1|b:8QOA|1|b = 0.04968FTO|1|b:8B0X|1|b = 0.04158FTO|1|b:7K00|1|b = 0.03158FTO|1|b:8FTO|1|b = 08FTO|1|b:9GHE|1|b = 0.03088FTO|1|b:8AYE|1|b = 0.02968FTO|1|b:8CGV|1|b = 0.04598FTO|1|b:8CEU|1|b = 0.04078FTO|1|b:8CGD|1|b = 0.04278FTO|1|b:8CAM|1|b = 0.04268FTO|1|b:8CGK|1|b = 0.03588FTO|1|b:8E30|1|J = 0.05348FTO|1|b:8E3O|1|J = 0.06299GHE|1|b:9D89|1|E = 0.06609GHE|1|b:8QOA|1|b = 0.04369GHE|1|b:8B0X|1|b = 0.03319GHE|1|b:7K00|1|b = 0.03009GHE|1|b:8FTO|1|b = 0.03089GHE|1|b:9GHE|1|b = 09GHE|1|b:8AYE|1|b = 0.02499GHE|1|b:8CGV|1|b = 0.04439GHE|1|b:8CEU|1|b = 0.03619GHE|1|b:8CGD|1|b = 0.03589GHE|1|b:8CAM|1|b = 0.03179GHE|1|b:8CGK|1|b = 0.02859GHE|1|b:8E30|1|J = 0.05689GHE|1|b:8E3O|1|J = 0.06338AYE|1|b:9D89|1|E = 0.06518AYE|1|b:8QOA|1|b = 0.04198AYE|1|b:8B0X|1|b = 0.03118AYE|1|b:7K00|1|b = 0.02618AYE|1|b:8FTO|1|b = 0.02968AYE|1|b:9GHE|1|b = 0.02498AYE|1|b:8AYE|1|b = 08AYE|1|b:8CGV|1|b = 0.02808AYE|1|b:8CEU|1|b = 0.03248AYE|1|b:8CGD|1|b = 0.04148AYE|1|b:8CAM|1|b = 0.07318AYE|1|b:8CGK|1|b = 0.06408AYE|1|b:8E30|1|J = 0.05568AYE|1|b:8E3O|1|J = 0.06268CGV|1|b:9D89|1|E = 0.08658CGV|1|b:8QOA|1|b = 0.06468CGV|1|b:8B0X|1|b = 0.03928CGV|1|b:7K00|1|b = 0.04198CGV|1|b:8FTO|1|b = 0.04598CGV|1|b:9GHE|1|b = 0.04438CGV|1|b:8AYE|1|b = 0.02808CGV|1|b:8CGV|1|b = 08CGV|1|b:8CEU|1|b = 0.03168CGV|1|b:8CGD|1|b = 0.05808CGV|1|b:8CAM|1|b = 0.08228CGV|1|b:8CGK|1|b = 0.06788CGV|1|b:8E30|1|J = 0.09728CGV|1|b:8E3O|1|J = 0.10288CEU|1|b:9D89|1|E = 0.06498CEU|1|b:8QOA|1|b = 0.05108CEU|1|b:8B0X|1|b = 0.04998CEU|1|b:7K00|1|b = 0.03738CEU|1|b:8FTO|1|b = 0.04078CEU|1|b:9GHE|1|b = 0.03618CEU|1|b:8AYE|1|b = 0.03248CEU|1|b:8CGV|1|b = 0.03168CEU|1|b:8CEU|1|b = 08CEU|1|b:8CGD|1|b = 0.03558CEU|1|b:8CAM|1|b = 0.07748CEU|1|b:8CGK|1|b = 0.06968CEU|1|b:8E30|1|J = 0.05838CEU|1|b:8E3O|1|J = 0.06168CGD|1|b:9D89|1|E = 0.07258CGD|1|b:8QOA|1|b = 0.05858CGD|1|b:8B0X|1|b = 0.06048CGD|1|b:7K00|1|b = 0.04528CGD|1|b:8FTO|1|b = 0.04278CGD|1|b:9GHE|1|b = 0.03588CGD|1|b:8AYE|1|b = 0.04148CGD|1|b:8CGV|1|b = 0.05808CGD|1|b:8CEU|1|b = 0.03558CGD|1|b:8CGD|1|b = 08CGD|1|b:8CAM|1|b = 0.02928CGD|1|b:8CGK|1|b = 0.04048CGD|1|b:8E30|1|J = 0.06178CGD|1|b:8E3O|1|J = 0.06288CAM|1|b:9D89|1|E = 0.07528CAM|1|b:8QOA|1|b = 0.08828CAM|1|b:8B0X|1|b = 0.08218CAM|1|b:7K00|1|b = 0.07558CAM|1|b:8FTO|1|b = 0.04268CAM|1|b:9GHE|1|b = 0.03178CAM|1|b:8AYE|1|b = 0.07318CAM|1|b:8CGV|1|b = 0.08228CAM|1|b:8CEU|1|b = 0.07748CAM|1|b:8CGD|1|b = 0.02928CAM|1|b:8CAM|1|b = 08CAM|1|b:8CGK|1|b = 0.03158CAM|1|b:8E30|1|J = 0.03938CAM|1|b:8E3O|1|J = 0.05498CGK|1|b:9D89|1|E = 0.08498CGK|1|b:8QOA|1|b = 0.10878CGK|1|b:8B0X|1|b = 0.06998CGK|1|b:7K00|1|b = 0.06798CGK|1|b:8FTO|1|b = 0.03588CGK|1|b:9GHE|1|b = 0.02858CGK|1|b:8AYE|1|b = 0.06408CGK|1|b:8CGV|1|b = 0.06788CGK|1|b:8CEU|1|b = 0.06968CGK|1|b:8CGD|1|b = 0.04048CGK|1|b:8CAM|1|b = 0.03158CGK|1|b:8CGK|1|b = 08CGK|1|b:8E30|1|J = 0.03938CGK|1|b:8E3O|1|J = 0.05648E30|1|J:9D89|1|E = 0.07128E30|1|J:8QOA|1|b = 0.06468E30|1|J:8B0X|1|b = 0.06038E30|1|J:7K00|1|b = 0.05718E30|1|J:8FTO|1|b = 0.05348E30|1|J:9GHE|1|b = 0.05688E30|1|J:8AYE|1|b = 0.05568E30|1|J:8CGV|1|b = 0.09728E30|1|J:8CEU|1|b = 0.05838E30|1|J:8CGD|1|b = 0.06178E30|1|J:8CAM|1|b = 0.03938E30|1|J:8CGK|1|b = 0.03938E30|1|J:8E30|1|J = 08E30|1|J:8E3O|1|J = 0.02988E3O|1|J:9D89|1|E = 0.07738E3O|1|J:8QOA|1|b = 0.07228E3O|1|J:8B0X|1|b = 0.07148E3O|1|J:7K00|1|b = 0.06648E3O|1|J:8FTO|1|b = 0.06298E3O|1|J:9GHE|1|b = 0.06338E3O|1|J:8AYE|1|b = 0.06268E3O|1|J:8CGV|1|b = 0.10288E3O|1|J:8CEU|1|b = 0.06168E3O|1|J:8CGD|1|b = 0.06288E3O|1|J:8CAM|1|b = 0.05498E3O|1|J:8CGK|1|b = 0.05648E3O|1|J:8E30|1|J = 0.02988E3O|1|J:8E3O|1|J = 09D89|1|E8QOA|1|b8B0X|1|b7K00|1|b8FTO|1|b9GHE|1|b8AYE|1|b8CGV|1|b8CEU|1|b8CGD|1|b8CAM|1|b8CGK|1|b8E30|1|J8E3O|1|JDiscrepancy0.000.020.040.060.080.10

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