RNA 3D Hub //

Equivalence class NR_3.5_41610.25 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19FY2|1|A (rep)Large subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-siteElectron microscopy2.327292026-01-14
29FY1|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-siteElectron microscopy2.327292026-01-14
39FY3|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-siteElectron microscopy2.827242026-01-14
47AQC|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of the bacterial RQC complex (Decoding State)Electron microscopy2.9928202020-11-25
57AS8|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOElectron microscopy2.928122020-12-09
68BUU|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541ARE-ABCF VmlR2 bound to a 70S ribosomeElectron microscopy2.928522023-04-05
79P38|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541YsxC-GMPPNP treated 44.5SYsxC particles. Class 1.Electron microscopy2.521162025-11-12
87AQD|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of the bacterial RQC complex (Translocating State)Electron microscopy3.129182020-11-25
96HA1|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinElectron microscopy3.128872018-08-29
107SAE|1|ALarge subunit ribosomal RNARNA (2434-MER)Bacillus subtilisBacteriaRF0254144SR70P Class1 ribosomal particleElectron microscopy324342022-03-02
119P4I|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541YsxC-GTP treated 44.5SYsxC particles. Class 5.Electron microscopy2.828182025-11-12
128QPP|1|XLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.428872023-12-27
137O5B|1|XLarge subunit ribosomal RNA23S rRNA (2887-MER)Bacillus subtilis subsp. subtilis str. 168BacteriaRF02541Cryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundElectron microscopy3.3328872022-02-02
147QV1|1|VLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis collided disome (Leading 70S)Electron microscopy3.528872022-03-09
157QV2|1|VLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis collided disome (Collided 70S)Electron microscopy3.528872022-03-09
169BSS|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF0254145SRbgA particle in complex with RbgA and YphC. Class BElectron microscopy3.125722024-12-25
177OPE|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)Electron microscopy3.228142021-07-21
187S9U|1|ALarge subunit ribosomal RNARNA (2436-MER)Bacillus subtilisBacteriaRF0254144SR3C ribosomal particleElectron microscopy3.224362022-03-02
197AS9|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH.Electron microscopy3.528122020-12-23
206HA8|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeElectron microscopy3.528872018-08-29
219BSL|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF0254145SRbgA particle in complex with RbgA and YphC. Class AElectron microscopy3.124142024-12-25
229BS0|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541YphC-treated 45SYphC particle. Class 5Electron microscopy3.326782024-12-25
236PPF|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Bacterial 45SRbgA ribosomal particle class BElectron microscopy3.424712019-09-18
246PVK|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Bacterial 45SRbgA ribosomal particle class AElectron microscopy3.421692019-09-18
257ASA|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOElectron microscopy3.5822020-12-23
266TNN|1|ULarge subunit ribosomal RNApre-23S rRNABacillus subtilisBacteriaRF02541Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAElectron microscopy3.0729302020-09-30
276TPQ|1|ULarge subunit ribosomal RNApre-23S rRNABacillus subtilisBacteriaRF02541RNase M5 bound to 50S ribosome with precursor 5S rRNAElectron microscopy3.0729242020-09-30
288S1P|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541YlmH bound to PtRNA-50SElectron microscopy1.9627332024-06-12
298QCQ|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541B. subtilis ApdA-stalled ribosomal complexElectron microscopy2.327452024-03-20
308S1U|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541YlmH bound to stalled 50S subunits with RqcH and PtRNAElectron microscopy3.427892024-06-12

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
19BS0|1|AYphC-treated 45SYphC particle. Class 5ELECTRON MICROSCOPY3.32678
29BSL|1|A45SRbgA particle in complex with RbgA and YphC. Class AELECTRON MICROSCOPY3.12414
39BSS|1|A45SRbgA particle in complex with RbgA and YphC. Class BELECTRON MICROSCOPY3.12572
49P38|1|AYsxC-GMPPNP treated 44.5SYsxC particles. Class 1.ELECTRON MICROSCOPY2.52116
59P4I|1|AYsxC-GTP treated 44.5SYsxC particles. Class 5.ELECTRON MICROSCOPY2.82818
67S9U|1|A44SR3C ribosomal particleELECTRON MICROSCOPY3.22436
77SAE|1|A44SR70P Class1 ribosomal particleELECTRON MICROSCOPY32434
86TPQ|1|URNase M5 bound to 50S ribosome with precursor 5S rRNAELECTRON MICROSCOPY3.072924
96TNN|1|UMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAELECTRON MICROSCOPY3.072930
106PPF|1|ABacterial 45SRbgA ribosomal particle class BELECTRON MICROSCOPY3.42471
116PVK|1|ABacterial 45SRbgA ribosomal particle class AELECTRON MICROSCOPY3.42169
127AQD|1|AStructure of the bacterial RQC complex (Translocating State)ELECTRON MICROSCOPY3.12918
137AQC|1|AStructure of the bacterial RQC complex (Decoding State)ELECTRON MICROSCOPY2.992820
147QV1|1|VBacillus subtilis collided disome (Leading 70S)ELECTRON MICROSCOPY3.52887
158QPP|1|XBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.42887
167O5B|1|XCryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundELECTRON MICROSCOPY3.332887
177AS9|1|ABacillus subtilis ribosome-associated quality control complex state A. Ribosomal 50S subunit with peptidyl tRNA in the A/P position and RqcH.ELECTRON MICROSCOPY3.52812
186HA8|1|ACryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeELECTRON MICROSCOPY3.52887
198BUU|1|AARE-ABCF VmlR2 bound to a 70S ribosomeELECTRON MICROSCOPY2.92852
208S1U|1|AYlmH bound to stalled 50S subunits with RqcH and PtRNAELECTRON MICROSCOPY3.42789
218S1P|1|AYlmH bound to PtRNA-50SELECTRON MICROSCOPY1.962733
227QV2|1|VBacillus subtilis collided disome (Collided 70S)ELECTRON MICROSCOPY3.52887
239FY3|1|AStructure of CliM-stalled Bacillus subtilis 70S ribosome with tRNA-Tyr in the A-siteELECTRON MICROSCOPY2.82724
249FY1|1|AStructure of CliM-stalled Bacillus subtilis 70S ribosome with release factor bound in the A-siteELECTRON MICROSCOPY2.32729
259FY2|1|AStructure of CliM-stalled Bacillus subtilis 70S ribosome with empty A-siteELECTRON MICROSCOPY2.32729
268QCQ|1|AB. subtilis ApdA-stalled ribosomal complexELECTRON MICROSCOPY2.32745
276HA1|1|ACryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinELECTRON MICROSCOPY3.12887
287OPE|1|ARqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)ELECTRON MICROSCOPY3.22814
297AS8|1|ABacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOELECTRON MICROSCOPY2.92812
307ASA|1|ABacillus subtilis ribosome-associated quality control complex state B, multibody refinement focussed on RqcH. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOELECTRON MICROSCOPY3.582

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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