RNA 3D Hub //

Equivalence class NR_all_41610.18 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
18BUU|1|A (rep)Large subunit ribosomal RNA23S rRNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541ARE-ABCF VmlR2 bound to a 70S ribosomeElectron microscopy2.92023-04-05
26TPQ|1|ULarge subunit ribosomal RNApre-23S rRNABacillus subtilisBacteriaRF02541RNase M5 bound to 50S ribosome with precursor 5S rRNAElectron microscopy3.072020-09-30
37AQD|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of the bacterial RQC complex (Translocating State)Electron microscopy3.12020-11-25
47AQC|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Structure of the bacterial RQC complex (Decoding State)Electron microscopy2.992020-11-25
56TNN|1|ULarge subunit ribosomal RNApre-23S rRNABacillus subtilisBacteriaRF02541Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAElectron microscopy3.072020-09-30
67AS8|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 microscopy2.92020-12-09
76HA1|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 microscopy3.12018-08-29
87O5B|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 microscopy3.332022-02-02
98QPP|1|XLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.42023-12-27
107OPE|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 microscopy3.22021-07-21
117QV1|1|VLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis collided disome (Leading 70S)Electron microscopy3.52022-03-09
127QV2|1|VLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis collided disome (Collided 70S)Electron microscopy3.52022-03-09
138R55|1|XLarge subunit ribosomal RNA23S RNA (2887-MER)Bacillus subtilisBacteriaRF02541Bacillus subtilis MutS2-collided disome complex (stalled 70S)Electron microscopy3.572024-01-17
147AS9|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 microscopy3.52020-12-23
156HA8|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Cryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeElectron microscopy3.52018-08-29
167SAE|1|ALarge subunit ribosomal RNARNA (2434-MER)Bacillus subtilisBacteriaRF0254144SR70P Class1 ribosomal particleElectron microscopy32022-03-02
175NJT|1|ULarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.Electron microscopy3.82017-06-14
183J9W|1|BALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Cryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexElectron microscopy3.92015-04-29
197S9U|1|ALarge subunit ribosomal RNARNA (2436-MER)Bacillus subtilisBacteriaRF0254144SR3C ribosomal particleElectron microscopy3.22022-03-02
206PPF|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Bacterial 45SRbgA ribosomal particle class BElectron microscopy3.42019-09-18
216PVK|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Bacterial 45SRbgA ribosomal particle class AElectron microscopy3.42019-09-18
226HTQ|1|ALarge subunit ribosomal RNA23S ribosomal RNABacillus subtilisBacteriaRF02541Stringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosomeElectron microscopy4.52019-10-23
237QGU|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Structure of the B. subtilis disome - stalled 70S ribosomeElectron microscopy4.752022-03-16
246PPK|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541RbgA+45SRbgA complexElectron microscopy4.42019-09-18
257QV3|1|VLarge subunit ribosomal RNA23S ribosomal RNABacillus subtilis subsp. subtilis str. 168BacteriaRF02541Bacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)Electron microscopy5.142022-03-09
267QH4|1|ALarge subunit ribosomal RNA23S rRNABacillus subtilisBacteriaRF02541Structure of the B. subtilis disome - collided 70S ribosomeElectron microscopy5.452022-03-16
277ASA|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 microscopy3.52020-12-23
283J3W|1|ALarge subunit ribosomal RNAribosome RNA 23SBacillus subtilisBacteriaRF02541Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a)Electron microscopy10.72013-06-12
293J3V|1|ALarge subunit ribosomal RNAribosome RNA 23SBacillus subtilisBacteriaRF02541Atomic model of the immature 50S subunit from Bacillus subtilis (state I-a)Electron microscopy13.32013-06-12

Release history

Release3.3183.3193.3203.3213.3223.3233.3243.3253.326
Date2024-01-172024-01-242024-01-312024-02-072024-02-142024-02-212024-02-282024-03-062024-03-13

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5

#S - ordering by similarity (same as in the heat map).
#SPDBTitleMethodResolutionLength
13J3W|1|AAtomic model of the immature 50S subunit from Bacillus subtilis (state II-a)ELECTRON MICROSCOPY10.72685
23J3V|1|AAtomic model of the immature 50S subunit from Bacillus subtilis (state I-a)ELECTRON MICROSCOPY13.32884
37QV2|1|VBacillus subtilis collided disome (Collided 70S)ELECTRON MICROSCOPY3.52887
47S9U|1|A44SR3C ribosomal particleELECTRON MICROSCOPY3.22436
57SAE|1|A44SR70P Class1 ribosomal particleELECTRON MICROSCOPY32434
66TNN|1|UMini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNAELECTRON MICROSCOPY3.072930
76TPQ|1|URNase M5 bound to 50S ribosome with precursor 5S rRNAELECTRON MICROSCOPY3.072924
86PVK|1|ABacterial 45SRbgA ribosomal particle class AELECTRON MICROSCOPY3.42169
96PPF|1|ABacterial 45SRbgA ribosomal particle class BELECTRON MICROSCOPY3.42471
107QV3|1|VBacillus subtilis MutS2-collided disome complex (MutS2 conf.2; Leading 70S)ELECTRON MICROSCOPY5.142887
117QV1|1|VBacillus subtilis collided disome (Leading 70S)ELECTRON MICROSCOPY3.52887
127QGU|1|AStructure of the B. subtilis disome - stalled 70S ribosomeELECTRON MICROSCOPY4.752923
135NJT|1|UStructure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.ELECTRON MICROSCOPY3.82923
143J9W|1|BACryo-EM structure of the Bacillus subtilis MifM-stalled ribosome complexELECTRON MICROSCOPY3.92923
157QH4|1|AStructure of the B. subtilis disome - collided 70S ribosomeELECTRON MICROSCOPY5.452923
166PPK|1|ARbgA+45SRbgA complexELECTRON MICROSCOPY4.42658
177AQD|1|AStructure of the bacterial RQC complex (Translocating State)ELECTRON MICROSCOPY3.12918
187AQC|1|AStructure of the bacterial RQC complex (Decoding State)ELECTRON MICROSCOPY2.992820
198R55|1|XBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.572887
208QPP|1|XBacillus subtilis MutS2-collided disome complex (stalled 70S)ELECTRON MICROSCOPY3.42887
217O5B|1|XCryo-EM structure of a Bacillus subtilis MifM-stalled ribosome-nascent chain complex with (p)ppGpp-SRP boundELECTRON MICROSCOPY3.332887
227AS9|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
238BUU|1|AARE-ABCF VmlR2 bound to a 70S ribosomeELECTRON MICROSCOPY2.92850
246HA8|1|ACryo-EM structure of the ABCF protein VmlR bound to the Bacillus subtilis ribosomeELECTRON MICROSCOPY3.52887
256HTQ|1|AStringent response control by a bifunctional RelA enzyme in the presence and absence of the ribosomeELECTRON MICROSCOPY4.52887
266HA1|1|ACryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycinELECTRON MICROSCOPY3.12887
277OPE|1|ARqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement)ELECTRON MICROSCOPY3.22814
287AS8|1|ABacillus subtilis ribosome quality control complex state B. Ribosomal 50S subunit with P-tRNA, RqcH, and RqcP/YabOELECTRON MICROSCOPY2.92812
297ASA|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
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