RNA 3D Hub //

Equivalence class NR_4.0_65061.13 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
16ZMI|1|L5+ 6ZMI|1|L8 (rep)Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complexElectron microscopy2.62020-08-19
26ZM7|1|L5+ 6ZM7|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complexElectron microscopy2.72020-07-29
37F5S|1|L5+ 7F5S|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002human delta-METTL18 60S ribosomeElectron microscopy2.722022-06-22
46Y6X|1|L5+ 6Y6X|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Tetracenomycin X bound to the human ribosomeElectron microscopy2.82020-07-08
56Z6N|1|L5+ 6Z6N|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1)Electron microscopy2.92020-07-29
66QZP|1|L5+ 6QZP|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA (3773-MER), 5.8S rRNA (156-MER)Homo sapiensEukaryaRF02543 + RF00002High-resolution cryo-EM structure of the human 80S ribosomeElectron microscopy2.92019-04-24
76ZME|1|L5+ 6ZME|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complexElectron microscopy32020-08-12
86Z6L|1|L5+ 6Z6L|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of human CCDC124 bound to 80S ribosomesElectron microscopy32020-07-29
96XA1|1|L5+ 6XA1|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Structure of a drug-like compound stalled human translation termination complexElectron microscopy2.82020-10-07
106ZMO|1|L5+ 6ZMO|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complexElectron microscopy3.12020-08-19
116Z6M|1|L5+ 6Z6M|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1Electron microscopy3.12020-07-29
126OLE|1|t+ 6OLE|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAsElectron microscopy3.12019-06-19
136OM0|1|t+ 6OM0|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAsElectron microscopy3.12019-06-19
146Y2L|1|L5+ 6Y2L|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of human ribosome in POST stateElectron microscopy32020-04-15
156LQM|1|2+ 6LQM|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of a pre-60S ribosomal subunit - state CElectron microscopy3.092020-08-26
166Y0G|1|L5+ 6Y0G|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of human ribosome in classical-PRE stateElectron microscopy3.22020-04-15
177BHP|1|L5+ 7BHP|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human Ebp1 - 80S ribosomeElectron microscopy3.32021-02-03
186LU8|1|2+ 6LU8|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of a human pre-60S ribosomal subunit - state AElectron microscopy3.132020-08-26
196LSR|1|2+ 6LSR|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of a pre-60S ribosomal subunit - state BElectron microscopy3.132020-08-26
206LSS|1|2+ 6LSS|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of a pre-60S ribosomal subunit - state preAElectron microscopy3.232020-08-26
216OLI|1|t+ 6OLI|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)Electron microscopy3.52019-06-19
226OLG|1|A2+ 6OLG|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)Electron microscopy3.42019-06-19
236Y57|1|L5+ 6Y57|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure of human ribosome in hybrid-PRE stateElectron microscopy3.52020-04-15
245T2C|1|A+ 5T2C|1|CLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAHomo sapiensEukaryaRF02543 + RF00002CryoEM structure of the human ribosome at 3.6 Angstrom resolutionElectron microscopy3.62017-01-25
256OM7|1|t+ 6OM7|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAsElectron microscopy3.72019-06-19
264UG0|1|L5+ 4UG0|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002STRUCTURE OF THE HUMAN 80S RIBOSOMEElectron microscopy3.62015-06-10
276OLF|1|t+ 6OLF|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAsElectron microscopy3.92019-06-19
286W6L|1|t+ 6W6L|1|DLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the human ribosome-TMCO1 transloconElectron microscopy3.842020-09-02
296IP5|1|1A+ 6IP5|1|1CLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)Electron microscopy3.92019-05-29
306IP8|1|1A+ 6IP8|1|1CLarge subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)Electron microscopy3.92019-05-29
316OLZ|1|A2+ 6OLZ|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNAElectron microscopy3.92019-06-19
325AJ0|1|A2+ 5AJ0|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Cryo electron microscopy of actively translating human polysomes (POST state).Electron microscopy3.52015-05-20
335LKS|1|L5+ 5LKS|1|L8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAHomo sapiensEukaryaRF02543 + RF00002Structure-function insights reveal the human ribosome as a cancer target for antibioticsElectron microscopy3.62017-04-26
346SXO|1|L5Large subunit ribosomal RNA28S ribosomal RNA including ES27L-B (2839-3265)Homo sapiensEukaryaRF02543Cryo-EM structure of the human Ebp1-ribosome complexElectron microscopy3.32020-02-19
355A8L|1|ALarge subunit ribosomal RNA28S RIBOSOMAL RNAHomo sapiensEukaryaRF02543Human eRF1 and the hCMV nascent peptide in the translation termination complexElectron microscopy3.82015-12-02

Release history

Release3.2363.2373.2383.2393.2403.2413.2423.2433.2443.2453.2463.2473.2483.2493.250
Date2022-06-222022-06-292022-07-062022-07-132022-07-202022-07-272022-08-032022-08-102022-08-172022-08-242022-08-312022-09-072022-09-142022-09-212022-09-28

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_4.0_65061.13NR_4.0_65061.123.236(34) 6OM0|1|t+6OM0|1|D, 6OLZ|1|A2+6OLZ|1|A3, 6OLI|1|t+6OLI|1|D, 6OLG|1|A2+6OLG|1|A3, 6OLF|1|t+6OLF|1|D, 6OLE|1|t+6OLE|1|D, 6LU8|1|2+6LU8|1|8, 6LSS|1|2+6LSS|1|8, 6LSR|1|2+6LSR|1|8, 6LQM|1|2+6LQM|1|8, 6IP8|1|1A+6IP8|1|1C, 6IP5|1|1A+6IP5|1|1C, 5T2C|1|A+5T2C|1|C, 5LKS|1|L5+5LKS|1|L8, 5AJ0|1|A2+5AJ0|1|A3, 5A8L|1|A, 7BHP|1|L5+7BHP|1|L8, 4UG0|1|L5+4UG0|1|L8, 6ZMO|1|L5+6ZMO|1|L8, 6ZMI|1|L5+6ZMI|1|L8, 6ZME|1|L5+6ZME|1|L8, 6ZM7|1|L5+6ZM7|1|L8, 6Z6N|1|L5+6Z6N|1|L8, 6Z6M|1|L5+6Z6M|1|L8, 6Z6L|1|L5+6Z6L|1|L8, 6Y6X|1|L5+6Y6X|1|L8, 6Y57|1|L5+6Y57|1|L8, 6Y2L|1|L5+6Y2L|1|L8, 6Y0G|1|L5+6Y0G|1|L8, 6XA1|1|L5+6XA1|1|L8, 6W6L|1|t+6W6L|1|D, 6SXO|1|L5, 6QZP|1|L5+6QZP|1|L8, 6OM7|1|t+6OM7|1|D(1) 7F5S|1|L5+7F5S|1|L8(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_4.0_65061.13NR_4.0_65061.143.251(35) 7F5S|1|L5+7F5S|1|L8, 5AJ0|1|A2+5AJ0|1|A3, 6QZP|1|L5+6QZP|1|L8, 7BHP|1|L5+7BHP|1|L8, 5A8L|1|A, 6OM7|1|t+6OM7|1|D, 6ZMO|1|L5+6ZMO|1|L8, 4UG0|1|L5+4UG0|1|L8, 6OM0|1|t+6OM0|1|D, 6ZMI|1|L5+6ZMI|1|L8, 6OLZ|1|A2+6OLZ|1|A3, 6ZME|1|L5+6ZME|1|L8, 6OLI|1|t+6OLI|1|D, 6ZM7|1|L5+6ZM7|1|L8, 6OLG|1|A2+6OLG|1|A3, 6Z6N|1|L5+6Z6N|1|L8, 6OLF|1|t+6OLF|1|D, 6Z6M|1|L5+6Z6M|1|L8, 6OLE|1|t+6OLE|1|D, 6Z6L|1|L5+6Z6L|1|L8, 6LU8|1|2+6LU8|1|8, 6Y6X|1|L5+6Y6X|1|L8, 6LSS|1|2+6LSS|1|8, 6Y57|1|L5+6Y57|1|L8, 6LSR|1|2+6LSR|1|8, 6Y2L|1|L5+6Y2L|1|L8, 6LQM|1|2+6LQM|1|8, 6Y0G|1|L5+6Y0G|1|L8, 6IP8|1|1A+6IP8|1|1C, 6IP5|1|1A+6IP5|1|1C, 6XA1|1|L5+6XA1|1|L8, 5T2C|1|A+5T2C|1|C, 6W6L|1|t+6W6L|1|D, 5LKS|1|L5+5LKS|1|L8, 6SXO|1|L5(0) (1) 7OW7|1|A+7OW7|1|C

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
15A8L|1|AHuman eRF1 and the hCMV nascent peptide in the translation termination complexELECTRON MICROSCOPY3.8253
26LQM|1|2+6LQM|1|8Cryo-EM structure of a pre-60S ribosomal subunit - state CELECTRON MICROSCOPY3.093433
36Z6M|1|L5+6Z6M|1|L8Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1ELECTRON MICROSCOPY3.13772
46ZME|1|L5+6ZME|1|L8SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complexELECTRON MICROSCOPY33773
56ZMO|1|L5+6ZMO|1|L8SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complexELECTRON MICROSCOPY3.13773
66ZMI|1|L5+6ZMI|1|L8SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complexELECTRON MICROSCOPY2.63773
76ZM7|1|L5+6ZM7|1|L8SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complexELECTRON MICROSCOPY2.73773
86Z6L|1|L5+6Z6L|1|L8Cryo-EM structure of human CCDC124 bound to 80S ribosomesELECTRON MICROSCOPY33772
96Z6N|1|L5+6Z6N|1|L8Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1)ELECTRON MICROSCOPY2.93772
106Y6X|1|L5+6Y6X|1|L8Tetracenomycin X bound to the human ribosomeELECTRON MICROSCOPY2.83773
116Y57|1|L5+6Y57|1|L8Structure of human ribosome in hybrid-PRE stateELECTRON MICROSCOPY3.53574
127BHP|1|L5+7BHP|1|L8Cryo-EM structure of the human Ebp1 - 80S ribosomeELECTRON MICROSCOPY3.33644
136Y0G|1|L5+6Y0G|1|L8Structure of human ribosome in classical-PRE stateELECTRON MICROSCOPY3.23644
146Y2L|1|L5+6Y2L|1|L8Structure of human ribosome in POST stateELECTRON MICROSCOPY33613
156QZP|1|L5+6QZP|1|L8High-resolution cryo-EM structure of the human 80S ribosomeELECTRON MICROSCOPY2.93696
167F5S|1|L5+7F5S|1|L8human delta-METTL18 60S ribosomeELECTRON MICROSCOPY2.723575
176XA1|1|L5+6XA1|1|L8Structure of a drug-like compound stalled human translation termination complexELECTRON MICROSCOPY2.83390
186IP8|1|1A+6IP8|1|1CCryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)ELECTRON MICROSCOPY3.93667
196IP5|1|1A+6IP5|1|1CCryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)ELECTRON MICROSCOPY3.93717
206W6L|1|t+6W6L|1|DCryo-EM structure of the human ribosome-TMCO1 transloconELECTRON MICROSCOPY3.843510
216OM0|1|t+6OM0|1|DHuman ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAsELECTRON MICROSCOPY3.13607
226OLE|1|t+6OLE|1|DHuman ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAsELECTRON MICROSCOPY3.13607
236OLI|1|t+6OLI|1|DStructure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)ELECTRON MICROSCOPY3.53607
246OLF|1|t+6OLF|1|DHuman ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAsELECTRON MICROSCOPY3.93607
256OM7|1|t+6OM7|1|DHuman ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAsELECTRON MICROSCOPY3.73607
266OLZ|1|A2+6OLZ|1|A3Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNAELECTRON MICROSCOPY3.93643
276OLG|1|A2+6OLG|1|A3Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)ELECTRON MICROSCOPY3.43612
285AJ0|1|A2+5AJ0|1|A3Cryo electron microscopy of actively translating human polysomes (POST state).ELECTRON MICROSCOPY3.53612
294UG0|1|L5+4UG0|1|L8STRUCTURE OF THE HUMAN 80S RIBOSOMEELECTRON MICROSCOPY3.63776
305T2C|1|A+5T2C|1|CCryoEM structure of the human ribosome at 3.6 Angstrom resolutionELECTRON MICROSCOPY3.63776
315LKS|1|L5+5LKS|1|L8Structure-function insights reveal the human ribosome as a cancer target for antibioticsELECTRON MICROSCOPY3.63776
326LSS|1|2+6LSS|1|8Cryo-EM structure of a pre-60S ribosomal subunit - state preAELECTRON MICROSCOPY3.233383
336LU8|1|2+6LU8|1|8Cryo-EM structure of a human pre-60S ribosomal subunit - state AELECTRON MICROSCOPY3.133386
346LSR|1|2+6LSR|1|8Cryo-EM structure of a pre-60S ribosomal subunit - state BELECTRON MICROSCOPY3.133384
356SXO|1|L5Cryo-EM structure of the human Ebp1-ribosome complexELECTRON MICROSCOPY3.3268
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