RNA 3D Hub //

Equivalence class NR_2.5_65061.53 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18GLP|1|L5+ 8GLP|1|L8 (rep)Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)Electron microscopy1.6737022023-04-19
28QYX|1|A2+ 8QYX|1|C2Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Human 60S ribosomal subunitElectron microscopy1.7838622024-12-11
38YOO|1|L5+ 8YOO|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineElectron microscopy238262024-07-10
48QFD|1|5+ 8QFD|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002UFL1 E3 ligase bound 60S ribosomeElectron microscopy2.232742024-02-21
59SPI|1|L5+ 9SPI|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEElectron microscopy2.435622026-01-21
69C3H|1|L5+ 9C3H|1|L1Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.Electron microscopy236792024-12-04
78A3D|1|A+ 8A3D|1|CLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human mature large subunit of the ribosome with eIF6 and homoharringtonine boundElectron microscopy1.6734512023-03-08
89SPF|1|L5+ 9SPF|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEElectron microscopy2.436222026-01-21
99S3D|1|L5+ 9S3D|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002NAC bound human RNC with 58 amino acid ARF1-linkerElectron microscopy2.3238042026-02-18
109I2D|1|L5+ 9I2D|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerElectron microscopy2.1938042026-02-04
119S3B|1|L5+ 9S3B|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1Electron microscopy2.3838042026-02-18
129S3C|1|L5+ 9S3C|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2Electron microscopy2.4238042026-02-18
139QLO|1|L5+ 9QLO|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002NMT1-NAC bound human RNC with full length ARF1 - State 1Electron microscopy2.4738042026-02-18
149PBE|1|L5+ 9PBE|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNA [Homo sapiens]Homo sapiensEukaryaRF02543 + RF00002In situ human 80S ribosome (composite map)Electron microscopy2.1938112025-12-24
158G5Y|1|L5+ 8G5Y|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)Electron microscopy2.2938772023-04-19
168YOP|1|L5+ 8YOP|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineElectron microscopy2.239272024-07-10
178QOI|1|L5+ 8QOI|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA (3773-MER), 5.8S rRNA (156-MER)Homo sapiensEukaryaRF02543 + RF00002Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNAElectron microscopy1.939292024-06-12
189P8B|1|L5+ 9P8B|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002In situ human eEF1A-A/T-P-E state 80S ribosomeElectron microscopy2.4838112025-12-24
198JDK|1|D+ 8JDK|1|FLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)Electron microscopy2.2636682023-12-06
209RPV|1|M5+ 9RPV|1|M8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA of the stalled 80S, 5.8S rRNA of the stalled 80SHomo sapiensEukaryaRF02543 + RF00002Structure of the ZAK-bound human disomeElectron microscopy2.3537022025-12-10
219GUL|1|L5+ 9GUL|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complexElectron microscopy2.238232025-09-24
228XSX|1|L5+ 8XSX|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2Electron microscopy2.439272024-07-10
238JDL|1|D+ 8JDL|1|FLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)Electron microscopy2.4236682023-12-06
248JDJ|1|D+ 8JDJ|1|FLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)Electron microscopy2.536682023-12-06
258K2C|1|L5+ 8K2C|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human 80S ribosome with TigecyclineElectron microscopy2.439272024-07-10
269RPV|1|L5+ 9RPV|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA of the collided 80S, 5.8S rRNA of the collided 80SHomo sapiensEukaryaRF02543 + RF00002Structure of the ZAK-bound human disomeElectron microscopy2.3537392025-12-10
277XNY|1|L1+ 7XNY|1|L3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsElectron microscopy2.539292023-04-05
288FLE|1|L3+ 8FLE|1|L1Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Human nuclear pre-60S ribosomal subunit (State L2)Electron microscopy2.4835262023-07-12
297OW7|1|A+ 7OW7|1|CLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002EIF6-bound large subunit of the human ribosomeElectron microscopy2.234512022-10-05
308FKV|1|L3+ 8FKV|1|L1Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Human nucleolar pre-60S ribosomal subunit (State D1)Electron microscopy2.4723652023-07-12
318FKW|1|L3+ 8FKW|1|L1Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Human nucleolar pre-60S ribosomal subunit (State D2)Electron microscopy2.524292023-07-12
329AZC|1|L5+ 9AZC|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002In situ human 80S ribosome (Consensus map)Electron microscopy2.1938962025-04-30

Release history

Release4.27
Date2026-02-18

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

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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
18QYX|1|A2+ 8QYX|1|C2Human 60S ribosomal subunitELECTRON MICROSCOPY1.783862
29SPI|1|L5+ 9SPI|1|L8CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEELECTRON MICROSCOPY2.43562
39SPF|1|L5+ 9SPF|1|L8CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEELECTRON MICROSCOPY2.43622
49RPV|1|M5+ 9RPV|1|M8Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.353702
58GLP|1|L5+ 8GLP|1|L8mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)ELECTRON MICROSCOPY1.673702
68G5Y|1|L5+ 8G5Y|1|L8mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)ELECTRON MICROSCOPY2.293877
78A3D|1|A+ 8A3D|1|CHuman mature large subunit of the ribosome with eIF6 and homoharringtonine boundELECTRON MICROSCOPY1.673451
87OW7|1|A+ 7OW7|1|CEIF6-bound large subunit of the human ribosomeELECTRON MICROSCOPY2.23451
98QOI|1|L5+ 8QOI|1|L8Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNAELECTRON MICROSCOPY1.93929
109C3H|1|L5+ 9C3H|1|L1Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.ELECTRON MICROSCOPY23679
119I2D|1|L5+ 9I2D|1|L8NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerELECTRON MICROSCOPY2.193804
129S3B|1|L5+ 9S3B|1|L8NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1ELECTRON MICROSCOPY2.383804
139S3C|1|L5+ 9S3C|1|L8NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2ELECTRON MICROSCOPY2.423804
149S3D|1|L5+ 9S3D|1|L8NAC bound human RNC with 58 amino acid ARF1-linkerELECTRON MICROSCOPY2.323804
159QLO|1|L5+ 9QLO|1|L8NMT1-NAC bound human RNC with full length ARF1 - State 1ELECTRON MICROSCOPY2.473804
169P8B|1|L5+ 9P8B|1|L8In situ human eEF1A-A/T-P-E state 80S ribosomeELECTRON MICROSCOPY2.483811
179PBE|1|L5+ 9PBE|1|L8In situ human 80S ribosome (composite map)ELECTRON MICROSCOPY2.193811
189AZC|1|L5+ 9AZC|1|L8In situ human 80S ribosome (Consensus map)ELECTRON MICROSCOPY2.193896
199RPV|1|L5+ 9RPV|1|L8Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.353739
208XSX|1|L5+ 8XSX|1|L8Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2ELECTRON MICROSCOPY2.43927
218YOO|1|L5+ 8YOO|1|L8Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineELECTRON MICROSCOPY23826
228K2C|1|L5+ 8K2C|1|L8Cryo-EM structure of the human 80S ribosome with TigecyclineELECTRON MICROSCOPY2.43927
238YOP|1|L5+ 8YOP|1|L8Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineELECTRON MICROSCOPY2.23927
247XNY|1|L1+ 7XNY|1|L3High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsELECTRON MICROSCOPY2.53929
258JDK|1|D+ 8JDK|1|FStructure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)ELECTRON MICROSCOPY2.263668
268JDJ|1|D+ 8JDJ|1|FStructure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)ELECTRON MICROSCOPY2.53668
278JDL|1|D+ 8JDL|1|FStructure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)ELECTRON MICROSCOPY2.423668
288QFD|1|5+ 8QFD|1|8UFL1 E3 ligase bound 60S ribosomeELECTRON MICROSCOPY2.23274
299GUL|1|L5+ 9GUL|1|L8Structure of FLuc-XBP1u+ stalled human 60S ribosome nascent chain complexELECTRON MICROSCOPY2.23823
308FLE|1|L3+ 8FLE|1|L1Human nuclear pre-60S ribosomal subunit (State L2)ELECTRON MICROSCOPY2.483526
318FKW|1|L3+ 8FKW|1|L1Human nucleolar pre-60S ribosomal subunit (State D2)ELECTRON MICROSCOPY2.52429
328FKV|1|L3+ 8FKV|1|L1Human nucleolar pre-60S ribosomal subunit (State D1)ELECTRON MICROSCOPY2.472365

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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