RNA 3D Hub //

Equivalence class NR_3.0_12763.31 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17QI4|1|A (rep)Large subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome at 2.2 A resolutionElectron microscopy2.2115582022-07-13
28RRI|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with antibiotic tigecyclineElectron microscopy2.415512025-03-12
36ZM6|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNAElectron microscopy2.5915312021-01-13
47OF0|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1).Electron microscopy2.213762021-06-09
57QI5|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolutionElectron microscopy2.6315582023-07-05
69CN3|1|ALarge subunit ribosomal RNA16S rRNAHomo sapiensMitochondriaRF02541Human 39S mitoribosome in complex with antibiotic LinezolidElectron microscopy2.6215272025-04-23
77O9M|1|ALarge subunit ribosomal RNA16S rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU moduleElectron microscopy2.514542021-06-30
87OF6|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 2).Electron microscopy2.614632021-06-09
98ANY|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNAElectron microscopy2.8515582023-08-16
108OIT|1|B8Large subunit ribosomal RNA16S rRNAHomo sapiensMitochondriaRF0254139S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNAElectron microscopy2.915582023-06-14
117OF4|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1).Electron microscopy2.714632021-06-09
126ZM5|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent polypeptideElectron microscopy2.8915342021-01-13
137OF7|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1).Electron microscopy2.513762021-06-23
147QI6|1|ALarge subunit ribosomal RNA16S mitochondrial rRNAHomo sapiensMitochondriaRF02541Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolutionElectron microscopy2.9815582023-05-17
156VMI|1|ALarge subunit ribosomal RNA16s rRNAHomo sapiensMitochondriaRF02541Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII)Electron microscopy2.9615272020-08-05
168K2A|1|L1Large subunit ribosomal RNA16S rRNAHomo sapiensMitochondriaRF02541Cryo-EM structure of the human 55S mitoribosome with TigecyclineElectron microscopy2.915002024-07-10
176VLZ|1|ALarge subunit ribosomal RNA16s rRNAHomo sapiensMitochondriaRF02541Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI)Electron microscopy2.9715272020-08-05
187OF2|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.Electron microscopy2.714102021-06-02
197OF3|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2).Electron microscopy2.713862021-05-19
207ODR|1|ALarge subunit ribosomal RNA16S mitochondrial rRNA, DNA (31-MER),16S mitochondrial rRNAHomo sapiensMitochondriaRF02541State A of the human mitoribosomal large subunit assembly intermediateElectron microscopy2.914482021-06-23
217OF5|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensMitochondriaRF02541Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2).Electron microscopy2.913892021-06-09
228QSJ|1|ALarge subunit ribosomal RNA16S rRNAHomo sapiensMitochondriaRF02541Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7Electron microscopy314182023-12-13
237PO4|1|ALarge subunit ribosomal RNA16SrRNAHomo sapiensMitochondriaRF02541Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP)Electron microscopy2.5611452022-06-15
247QH7|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensEukaryaRF02541Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4Electron microscopy2.8912562022-05-18
258QU5|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensEukaryaRF02541mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2Electron microscopy2.4210492024-06-26
268QU1|1|ALarge subunit ribosomal RNA16S ribosomal RNAHomo sapiensEukaryaRF02541mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1Electron microscopy2.749382024-06-26

Release history

Release3.3843.3853.3863.3873.3883.3893.3903.3913.3923.393
Date2025-04-232025-04-302025-05-072025-05-142025-05-212025-05-282025-06-042025-06-112025-06-182025-06-25

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
16VMI|1|AStructure of the human mitochondrial ribosome-EF-G1 complex (ClassIII)ELECTRON MICROSCOPY2.961527
26VLZ|1|AStructure of the human mitochondrial ribosome-EF-G1 complex (ClassI)ELECTRON MICROSCOPY2.971527
39CN3|1|AHuman 39S mitoribosome in complex with antibiotic LinezolidELECTRON MICROSCOPY2.621527
48QSJ|1|AHuman mitoribosomal large subunit assembly intermediate 2 with GTPBP7ELECTRON MICROSCOPY31418
58K2A|1|L1Cryo-EM structure of the human 55S mitoribosome with TigecyclineELECTRON MICROSCOPY2.91500
68RRI|1|AHuman mitochondrial ribosome in complex with antibiotic tigecyclineELECTRON MICROSCOPY2.41551
78OIT|1|B839S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNAELECTRON MICROSCOPY2.91558
87QI4|1|AHuman mitochondrial ribosome at 2.2 A resolutionELECTRON MICROSCOPY2.211558
97QI5|1|AHuman mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolutionELECTRON MICROSCOPY2.631558
108ANY|1|AHuman mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNAELECTRON MICROSCOPY2.851558
116ZM6|1|AHuman mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNAELECTRON MICROSCOPY2.591531
126ZM5|1|AHuman mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent polypeptideELECTRON MICROSCOPY2.891534
137QI6|1|AHuman mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolutionELECTRON MICROSCOPY2.981558
147OF6|1|AStructure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 2).ELECTRON MICROSCOPY2.61463
157OF4|1|AStructure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1).ELECTRON MICROSCOPY2.71463
167OF2|1|AStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.ELECTRON MICROSCOPY2.71410
177OF5|1|AStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2).ELECTRON MICROSCOPY2.91389
187OF7|1|AStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1).ELECTRON MICROSCOPY2.51376
198QU5|1|Amt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2ELECTRON MICROSCOPY2.421049
207PO4|1|AAssembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP)ELECTRON MICROSCOPY2.561145
218QU1|1|Amt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1ELECTRON MICROSCOPY2.74938
227QH7|1|ACryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4ELECTRON MICROSCOPY2.891256
237OF0|1|AStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1).ELECTRON MICROSCOPY2.21376
247OF3|1|AStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2).ELECTRON MICROSCOPY2.71386
257ODR|1|AState A of the human mitoribosomal large subunit assembly intermediateELECTRON MICROSCOPY2.91448
267O9M|1|AHuman mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU moduleELECTRON MICROSCOPY2.51454

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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