RNA 3D Hub //

Equivalence class NR_20.0_52752.17 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
18GLP|1|L7 (rep)5S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)Electron microscopy1.672023-04-19
28A3D|1|B5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human mature large subunit of the ribosome with eIF6 and homoharringtonine boundElectron microscopy1.672023-03-08
37OW7|1|B5S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001EIF6-bound large subunit of the human ribosomeElectron microscopy2.22022-10-05
48G5Y|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)Electron microscopy2.292023-04-19
57XNY|1|L25S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsElectron microscopy2.52023-04-05
68G60|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)Electron microscopy2.542023-04-19
76ZMI|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complexElectron microscopy2.62020-08-19
88G5Z|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)Electron microscopy2.642023-04-19
96ZM7|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complexElectron microscopy2.72020-07-29
107XNX|1|L25S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cellsElectron microscopy2.72023-04-05
117F5S|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001human delta-METTL18 60S ribosomeElectron microscopy2.722022-06-22
128G6J|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2)Electron microscopy2.82023-04-19
136XA1|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Structure of a drug-like compound stalled human translation termination complexElectron microscopy2.82020-10-07
146Y6X|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Tetracenomycin X bound to the human ribosomeElectron microscopy2.82020-07-08
156Z6N|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1)Electron microscopy2.92020-07-29
166QZP|1|L75S ribosomal RNA5S rRNA (120-MER)Homo sapiensEukaryaRF00001High-resolution cryo-EM structure of the human 80S ribosomeElectron microscopy2.92019-04-24
178G61|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state)Electron microscopy2.942023-04-19
186Z6L|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of human CCDC124 bound to 80S ribosomesElectron microscopy32020-07-29
196ZME|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complexElectron microscopy32020-08-12
207QVP|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human collided disome (di-ribosome) stalled on XBP1 mRNAElectron microscopy32022-10-12
217QVP|1|L95S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human collided disome (di-ribosome) stalled on XBP1 mRNAElectron microscopy32022-10-12
226LQM|1|55S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of a pre-60S ribosomal subunit - state CElectron microscopy3.092020-08-26
236Z6M|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1Electron microscopy3.12020-07-29
246ZMO|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complexElectron microscopy3.12020-08-19
256LSR|1|55S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of a pre-60S ribosomal subunit - state BElectron microscopy3.132020-08-26
266LU8|1|55S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of a human pre-60S ribosomal subunit - state AElectron microscopy3.132020-08-26
276OLE|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAsElectron microscopy3.12019-06-19
286Y2L|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Structure of human ribosome in POST stateElectron microscopy32020-04-15
296OM0|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAsElectron microscopy3.12019-06-19
306LSS|1|55S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Cryo-EM structure of a pre-60S ribosomal subunit - state preAElectron microscopy3.232020-08-26
316Y0G|1|L75S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001Structure of human ribosome in classical-PRE stateElectron microscopy3.22020-04-15
327BHP|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo-EM structure of the human Ebp1 - 80S ribosomeElectron microscopy3.32021-02-03
336OLG|1|A45S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)Electron microscopy3.42019-06-19
346OLI|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)Electron microscopy3.52019-06-19
356Y57|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Structure of human ribosome in hybrid-PRE stateElectron microscopy3.52020-04-15
365T2C|1|B5S ribosomal RNA5S rRNAHomo sapiensEukaryaRF00001CryoEM structure of the human ribosome at 3.6 Angstrom resolutionElectron microscopy3.62017-01-25
374UG0|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001STRUCTURE OF THE HUMAN 80S RIBOSOMEElectron microscopy3.62015-06-10
386OM7|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAsElectron microscopy3.72019-06-19
396W6L|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo-EM structure of the human ribosome-TMCO1 transloconElectron microscopy3.842020-09-02
406OLF|1|E5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAsElectron microscopy3.92019-06-19
416IP5|1|1B5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)Electron microscopy3.92019-05-29
426OLZ|1|A45S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNAElectron microscopy3.92019-06-19
436IP8|1|1B5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)Electron microscopy3.92019-05-29
445LKS|1|L75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Structure-function insights reveal the human ribosome as a cancer target for antibioticsElectron microscopy3.62017-04-26
455AJ0|1|A45S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo electron microscopy of actively translating human polysomes (POST state).Electron microscopy3.52015-05-20
466IP6|1|1B5S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii)Electron microscopy4.52019-05-29
474V6X|1|A75S ribosomal RNA5S ribosomal RNAHomo sapiensEukaryaRF00001Structure of the human 80S ribosomeElectron microscopy52014-07-09

Release history

Release3.2793.2803.2813.2823.2833.2843.2853.2863.2873.2883.2893.290
Date2023-04-192023-04-262023-05-032023-05-102023-05-172023-05-242023-05-312023-06-072023-06-142023-06-212023-06-282023-07-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_20.0_52752.17NR_20.0_52752.163.279(41) 7QVP|1|L7, 6LSR|1|5, 6Y6X|1|L7, 6OLG|1|A4, 6ZMI|1|L7, 5T2C|1|B, 6W6L|1|E, 6ZME|1|L7, 5LKS|1|L7, 6QZP|1|L7, 7OW7|1|B, 6LQM|1|5, 6Y57|1|L7, 8A3D|1|B, 6OLF|1|E, 6ZM7|1|L7, 5AJ0|1|A4, 6OM7|1|E, 6IP8|1|1B, 6Y2L|1|L7, 7F5S|1|L7, 7XNY|1|L2, 6OLE|1|E, 6Z6N|1|L7, 4V6X|1|A7, 6OM0|1|E, 6Y0G|1|L7, 7BHP|1|L7, 6IP6|1|1B, 7XNX|1|L2, 6LU8|1|5, 6Z6M|1|L7, 4UG0|1|L7, 6OLZ|1|A4, 6XA1|1|L7, 6ZMO|1|L7, 6IP5|1|1B, 7QVP|1|L9, 6LSS|1|5, 6Z6L|1|L7, 6OLI|1|E(6) 8G60|1|L7, 8G6J|1|L7, 8G5Y|1|L7, 8G5Z|1|L7, 8G61|1|L7, 8GLP|1|L7(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_20.0_52752.17NR_20.0_52752.183.291(47) 8GLP|1|L7, 6OLF|1|E, 6Z6M|1|L7, 6IP8|1|1B, 8A3D|1|B, 6W6L|1|E, 7F5S|1|L7, 4V6X|1|A7, 6OLG|1|A4, 6Z6N|1|L7, 6LQM|1|5, 8G5Z|1|L7, 6Y0G|1|L7, 7OW7|1|B, 5AJ0|1|A4, 6OLZ|1|A4, 6ZM7|1|L7, 6LSR|1|5, 8G60|1|L7, 6Y2L|1|L7, 7QVP|1|L9, 5LKS|1|L7, 6OM0|1|E, 6ZME|1|L7, 6LU8|1|5, 8G61|1|L7, 6Y57|1|L7, 7XNX|1|L2, 5T2C|1|B, 6OM7|1|E, 6ZMO|1|L7, 6OLE|1|E, 8G6J|1|L7, 6Y6X|1|L7, 6IP6|1|1B, 7XNY|1|L2, 6QZP|1|L7, 7BHP|1|L7, 8G5Y|1|L7, 6OLI|1|E, 7QVP|1|L7, 6LSS|1|5, 6ZMI|1|L7, 6IP5|1|1B, 6Z6L|1|L7, 4UG0|1|L7, 6XA1|1|L7(0) (13) 8FLF|1|L4, 8FLA|1|L4, 8FL3|1|L4, 8FL6|1|L4, 8FLD|1|L4, 8FL7|1|L4, 8FL0|1|L4, 8FLB|1|L4, 8FL4|1|L4, 8FLE|1|L4, 8FL9|1|L4, 8FL2|1|L4, 8FLC|1|L4

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
15LKS|1|L7Structure-function insights reveal the human ribosome as a cancer target for antibioticsELECTRON MICROSCOPY3.6120
26IP8|1|1BCryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv)ELECTRON MICROSCOPY3.9120
36IP5|1|1BCryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)ELECTRON MICROSCOPY3.9120
46IP6|1|1BCryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii)ELECTRON MICROSCOPY4.5120
55T2C|1|BCryoEM structure of the human ribosome at 3.6 Angstrom resolutionELECTRON MICROSCOPY3.6120
64UG0|1|L7STRUCTURE OF THE HUMAN 80S RIBOSOMEELECTRON MICROSCOPY3.6120
76LU8|1|5Cryo-EM structure of a human pre-60S ribosomal subunit - state AELECTRON MICROSCOPY3.13120
86LSS|1|5Cryo-EM structure of a pre-60S ribosomal subunit - state preAELECTRON MICROSCOPY3.23120
96LSR|1|5Cryo-EM structure of a pre-60S ribosomal subunit - state BELECTRON MICROSCOPY3.13120
106LQM|1|5Cryo-EM structure of a pre-60S ribosomal subunit - state CELECTRON MICROSCOPY3.09120
117XNX|1|L2High resolution cry-EM structure of the human 80S ribosome from SNORD127+/+ Kasumi-1 cellsELECTRON MICROSCOPY2.7120
127XNY|1|L2High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsELECTRON MICROSCOPY2.5120
136ZME|1|L7SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complexELECTRON MICROSCOPY3120
146ZMO|1|L7SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complexELECTRON MICROSCOPY3.1120
156ZM7|1|L7SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complexELECTRON MICROSCOPY2.7120
166ZMI|1|L7SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complexELECTRON MICROSCOPY2.6120
176Z6M|1|L7Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1ELECTRON MICROSCOPY3.1120
186Z6N|1|L7Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1)ELECTRON MICROSCOPY2.9120
196Z6L|1|L7Cryo-EM structure of human CCDC124 bound to 80S ribosomesELECTRON MICROSCOPY3120
206Y6X|1|L7Tetracenomycin X bound to the human ribosomeELECTRON MICROSCOPY2.8120
216XA1|1|L7Structure of a drug-like compound stalled human translation termination complexELECTRON MICROSCOPY2.8120
226QZP|1|L7High-resolution cryo-EM structure of the human 80S ribosomeELECTRON MICROSCOPY2.9120
237OW7|1|BEIF6-bound large subunit of the human ribosomeELECTRON MICROSCOPY2.2120
247F5S|1|L7human delta-METTL18 60S ribosomeELECTRON MICROSCOPY2.72120
258A3D|1|BHuman mature large subunit of the ribosome with eIF6 and homoharringtonine boundELECTRON MICROSCOPY1.67120
268GLP|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)ELECTRON MICROSCOPY1.67120
278G5Y|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)ELECTRON MICROSCOPY2.29120
288G60|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state)ELECTRON MICROSCOPY2.54120
298G6J|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2)ELECTRON MICROSCOPY2.8120
308G5Z|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state)ELECTRON MICROSCOPY2.64120
318G61|1|L7mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state)ELECTRON MICROSCOPY2.94120
327QVP|1|L7Human collided disome (di-ribosome) stalled on XBP1 mRNAELECTRON MICROSCOPY3120
336Y2L|1|L7Structure of human ribosome in POST stateELECTRON MICROSCOPY3120
346Y0G|1|L7Structure of human ribosome in classical-PRE stateELECTRON MICROSCOPY3.2120
356Y57|1|L7Structure of human ribosome in hybrid-PRE stateELECTRON MICROSCOPY3.5120
367QVP|1|L9Human collided disome (di-ribosome) stalled on XBP1 mRNAELECTRON MICROSCOPY3120
376OM0|1|EHuman ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAsELECTRON MICROSCOPY3.1119
386OLE|1|EHuman ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAsELECTRON MICROSCOPY3.1119
396OLI|1|EStructure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC)ELECTRON MICROSCOPY3.5119
406OM7|1|EHuman ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAsELECTRON MICROSCOPY3.7119
416OLF|1|EHuman ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAsELECTRON MICROSCOPY3.9119
426OLZ|1|A4Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNAELECTRON MICROSCOPY3.9119
436OLG|1|A4Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA)ELECTRON MICROSCOPY3.4119
445AJ0|1|A4Cryo electron microscopy of actively translating human polysomes (POST state).ELECTRON MICROSCOPY3.5119
457BHP|1|L7Cryo-EM structure of the human Ebp1 - 80S ribosomeELECTRON MICROSCOPY3.3120
466W6L|1|ECryo-EM structure of the human ribosome-TMCO1 transloconELECTRON MICROSCOPY3.84119
474V6X|1|A7Structure of the human 80S ribosomeELECTRON MICROSCOPY5121
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