RNA 3D Hub //

Equivalence class NR_all_97435.21 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19FY1|1|B (rep)5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-siteElectron microscopy2.31122026-01-14
29FY2|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-siteElectron microscopy2.31122026-01-14
39FY3|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-siteElectron microscopy2.81122026-01-14
47AS8|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 microscopy2.91122020-12-09
58BUU|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001ARE-ABCF VmlR2 bound to a 70S ribosomeElectron microscopy2.91122023-04-05
67AQC|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of the bacterial RQC complex (Decoding State)Electron microscopy2.991122020-11-25
76HA1|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinElectron microscopy3.11122018-08-29
88QPP|1|Y5S ribosomal RNA5S rRNA (112-MER)Bacillus subtilisBacteriaRF00001Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.41122023-12-27
97AQD|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Structure of the bacterial RQC complex (Translocating State)Electron microscopy3.11122020-11-25
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 microscopy3.21122021-07-21
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 microscopy3.331122022-02-02
127QV1|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis collided disome (Leading 70S)Electron microscopy3.51122022-03-09
138R55|1|Y5S ribosomal RNA5S rRNA (112-MER)Bacillus subtilisBacteriaRF00001Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.571122024-01-17
147QV2|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis collided disome (Collided 70S)Electron microscopy3.51122022-03-09
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 microscopy3.51122020-12-23
166HA8|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeElectron microscopy3.51122018-08-29
173J9W|1|BB5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexElectron microscopy3.91122015-04-29
185NJT|1|V5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.Electron microscopy3.81122017-06-14
196HTQ|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilisBacteriaRF00001Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosomeElectron microscopy4.51122019-10-23
209P4I|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001YsxC-GTP treated 44.5SYsxC particles. Class 5.Electron microscopy2.81122025-11-12
219BS0|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001YphC-treated 45SYphC particle. Class 5Electron microscopy3.31112024-12-25
226PPK|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001RbgA+45SRbgA complexElectron microscopy4.41122019-09-18
237QGU|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Structure of the B. subtilis disome - stalled 70S ribosomeElectron microscopy4.751122022-03-16
247QV3|1|B5S ribosomal RNA5S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)Electron microscopy5.141122022-03-09
256PPF|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Bacterial 45SRbgA ribosomal particle class BElectron microscopy3.41122019-09-18
267QH4|1|B5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Structure of the B. subtilis disome - collided 70S ribosomeElectron microscopy5.451122022-03-16
279BSS|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF0000145SRbgA particle in complex with RbgA and YphC. Class BElectron microscopy3.11122024-12-25
283J3V|1|B5S ribosomal RNAribosome RNA 5SBacillus subtilisBacteriaRF00001Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)Electron microscopy13.31192013-06-12
296TPQ|1|V5S ribosomal RNApre-5S rRNABacillus subtilisBacteriaRF00001RNase M5 bound to 50S ribosome with precursor 5S rRNAElectron microscopy3.071232020-09-30
306TNN|1|V5S ribosomal RNA5S rRNABacillus subtilisBacteriaRF00001Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAElectron microscopy3.071162020-09-30
318S1P|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001YlmH bound to PtRNA-50SElectron microscopy1.961122024-06-12
328QCQ|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001B. subtilis ApdA-stalled ribosomal complexElectron microscopy2.31122024-03-20
338S1U|1|B5S ribosomal RNA5S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF00001YlmH bound to stalled 50S subunits with RqcH and PtRNAElectron microscopy3.41122024-06-12

Release history

Release4.22
Date2026-01-14

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
13J3V|1|BAtomic model of the immature 50S subunit from Bacillus subtilis (state I-a)ELECTRON MICROSCOPY13.3119
26PPK|1|BRbgA+45SRbgA complexELECTRON MICROSCOPY4.4112
37QGU|1|BStructure of the B. subtilis disome - stalled 70S ribosomeELECTRON MICROSCOPY4.75112
47QH4|1|BStructure of the B. subtilis disome - collided 70S ribosomeELECTRON MICROSCOPY5.45112
53J9W|1|BBCryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexELECTRON MICROSCOPY3.9112
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
159FY3|1|BStructure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-siteELECTRON MICROSCOPY2.8112
169FY1|1|BStructure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-siteELECTRON MICROSCOPY2.3112
179FY2|1|BStructure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-siteELECTRON MICROSCOPY2.3112
188S1P|1|BYlmH bound to PtRNA-50SELECTRON MICROSCOPY1.96112
198S1U|1|BYlmH bound to stalled 50S subunits with RqcH and PtRNAELECTRON MICROSCOPY3.4112
206HA8|1|BCryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeELECTRON MICROSCOPY3.5112
216HA1|1|BCryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinELECTRON MICROSCOPY3.1112
227QV2|1|BBacillus subtilis collided disome (Collided 70S)ELECTRON MICROSCOPY3.5112
237QV1|1|BBacillus subtilis collided disome (Leading 70S)ELECTRON MICROSCOPY3.5112
247QV3|1|BBacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)ELECTRON MICROSCOPY5.14112
257O5B|1|YCryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundELECTRON MICROSCOPY3.33112
268QPP|1|YBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.4112
278R55|1|YBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.57112
286TNN|1|VMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAELECTRON MICROSCOPY3.07116
296TPQ|1|VRNase M5 bound to 50S ribosome with precursor 5S rRNAELECTRON MICROSCOPY3.07123
306PPF|1|BBacterial 45SRbgA ribosomal particle class BELECTRON MICROSCOPY3.4112
319P4I|1|BYsxC-GTP treated 44.5SYsxC particles. Class 5.ELECTRON MICROSCOPY2.8112
329BS0|1|BYphC-treated 45SYphC particle. Class 5ELECTRON MICROSCOPY3.3111
339BSS|1|B45SRbgA particle in complex with RbgA and YphC. Class BELECTRON MICROSCOPY3.1112

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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