RNA 3D Hub //

Equivalence class NR_20.0_97435.16 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
18S1P|1|B (rep)5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001YlmH bound to PtRNA-50SElectron microscopy1.962024-06-12
28QCQ|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001B. subtilis ApdA-stalled ribosomal complexElectron microscopy2.32024-03-20
36TPQ|1|V5S ribosomal RNApre-5S rRNABacillus subtilisBacteriaRF00001RNase M5 bound to 50S ribosome with precursor 5S rRNAElectron microscopy3.072020-09-30
48BUU|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001ARE-ABCF VmlR2 bound to a 70S ribosomeElectron microscopy2.92023-04-05
57AQC|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of the bacterial RQC complex (Decoding State)Electron microscopy2.992020-11-25
67AS8|1|B5S ribosomal RNA5s rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOElectron microscopy2.92020-12-09
77AQD|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of the bacterial RQC complex (Translocating State)Electron microscopy3.12020-11-25
86TNN|1|V5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAElectron microscopy3.072020-09-30
96HA1|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinElectron microscopy3.12018-08-29
107OPE|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)Electron microscopy3.22021-07-21
117O5B|1|Y5S ribosomal RNA5S rRNA (112-MER)Bacillus subtilis subsp. subtilis str. 168BacteriaRF00001Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundElectron microscopy3.332022-02-02
128S1U|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001YlmH bound to stalled 50S subunits with RqcH and PtRNAElectron microscopy3.42024-06-12
138QPP|1|Y5S ribosomal RNA5S rRNA (112-MER)Bacillus subtilisBacteriaRF00001Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.42023-12-27
147QV2|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis collided disome (Collided 70S)Electron microscopy3.52022-03-09
157AS9|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH.Electron microscopy3.52020-12-23
167QV1|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis collided disome (Leading 70S)Electron microscopy3.52022-03-09
176HA8|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeElectron microscopy3.52018-08-29
188R55|1|Y5S ribosomal RNA5S rRNA (112-MER)Bacillus subtilisBacteriaRF00001Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.572024-01-17
196PPF|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Bacterial 45SRbgA ribosomal particle class BElectron microscopy3.42019-09-18
205NJT|1|V5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.Electron microscopy3.82017-06-14
213J9W|1|BB5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexElectron microscopy3.92015-04-29
226HTQ|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosomeElectron microscopy4.52019-10-23
236PPK|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001RbgA+45SRbgA complexElectron microscopy4.42019-09-18
247QGU|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Structure of the B. subtilis disome - stalled 70S ribosomeElectron microscopy4.752022-03-16
257QV3|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)Electron microscopy5.142022-03-09
267QH4|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Structure of the B. subtilis disome - collided 70S ribosomeElectron microscopy5.452022-03-16
273J3V|1|B5S ribosomal RNAribosome RNA 5SBacillus subtilisBacteriaRF00001Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)Electron microscopy13.32013-06-12

Release history

Release3.3393.3403.3413.3423.3433.3443.3453.3463.3473.3483.3493.3503.3513.3523.3533.3543.3553.3563.3573.3583.3593.3603.3613.362
Date2024-06-122024-06-192024-06-262024-07-032024-07-102024-07-172024-07-252024-07-312024-08-072024-08-142024-08-212024-08-282024-09-042024-09-112024-09-182024-09-252024-10-022024-10-092024-10-162024-10-232024-10-302024-11-062024-11-132024-11-20

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.

#SViewPDBTitleMethodResolutionLength
16PPF|1|BBacterial 45SRbgA ribosomal particle class BELECTRON MICROSCOPY3.4112
26PPK|1|BRbgA+45SRbgA complexELECTRON MICROSCOPY4.4112
33J9W|1|BBCryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexELECTRON MICROSCOPY3.9112
47QH4|1|BStructure of the B. subtilis disome - collided 70S ribosomeELECTRON MICROSCOPY5.45112
57QGU|1|BStructure of the B. subtilis disome - stalled 70S ribosomeELECTRON MICROSCOPY4.75112
67AQC|1|BStructure of the bacterial RQC complex (Decoding State)ELECTRON MICROSCOPY2.99112
77AQD|1|BStructure of the bacterial RQC complex (Translocating State)ELECTRON MICROSCOPY3.1112
85NJT|1|VStructure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.ELECTRON MICROSCOPY3.8112
96HTQ|1|BStringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosomeELECTRON MICROSCOPY4.5112
107AS9|1|BBacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH.ELECTRON MICROSCOPY3.5112
117AS8|1|BBacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOELECTRON MICROSCOPY2.9112
127OPE|1|BRqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)ELECTRON MICROSCOPY3.2112
138BUU|1|BARE-ABCF VmlR2 bound to a 70S ribosomeELECTRON MICROSCOPY2.9112
148QCQ|1|BB. subtilis ApdA-stalled ribosomal complexELECTRON MICROSCOPY2.3112
158S1P|1|BYlmH bound to PtRNA-50SELECTRON MICROSCOPY1.96112
168S1U|1|BYlmH bound to stalled 50S subunits with RqcH and PtRNAELECTRON MICROSCOPY3.4112
176HA8|1|BCryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeELECTRON MICROSCOPY3.5112
186HA1|1|BCryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinELECTRON MICROSCOPY3.1112
197QV2|1|BBacillus subtilis collided disome (Collided 70S)ELECTRON MICROSCOPY3.5112
207QV1|1|BBacillus subtilis collided disome (Leading 70S)ELECTRON MICROSCOPY3.5112
217QV3|1|BBacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)ELECTRON MICROSCOPY5.14112
226TPQ|1|VRNase M5 bound to 50S ribosome with precursor 5S rRNAELECTRON MICROSCOPY3.07123
236TNN|1|VMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAELECTRON MICROSCOPY3.07116
247O5B|1|YCryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundELECTRON MICROSCOPY3.33112
258QPP|1|YBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.4112
268R55|1|YBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.57112
273J3V|1|BAtomic model of the immature 50S subunit from Bacillus subtilis (state I-a)ELECTRON MICROSCOPY13.3119

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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