RNA 3D Hub //

Equivalence class NR_4.0_06650.8 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
16D9J|1|5+ 6D9J|1|8 (rep)Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.Electron microscopy3.22018-06-06
21VWW|1|5+ 1VWW|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the mammalian 60S ribosomal subunit. This entry contains the large subunit ribosomal RNA.Electron microscopy3.42014-06-18
31VWY|1|5+ 1VWY|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the idle mammalian ribosome-Sec61 complex. This entry contains the large subunit ribosomal RNA.Electron microscopy3.42014-06-18
43J71|1|5+ 3J71|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the mammalian 60S ribosomal subunitElectron microscopy3.42014-06-18
53J72|1|5+ 3J72|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the idle mammalian ribosome-Sec61 complexElectron microscopy3.42014-06-18
65LZS|1|5+ 5LZS|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BElectron microscopy3.312016-11-30
71VX3|1|5+ 1VX3|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the 80S mammalian ribosome bound to eEF2. This entry contains the large subunit ribosomal RNA.Electron microscopy3.52014-06-18
83J74|1|5+ 3J74|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the 80S mammalian ribosome bound to eEF2Electron microscopy3.52014-06-18
95LZV|1|5+ 5LZV|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.Electron microscopy3.352016-11-30
106MTD|1|5+ 6MTD|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)Electron microscopy3.32018-11-21
116D90|1|5+ 6D90|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.Electron microscopy3.22018-06-06
126MTE|1|5+ 6MTE|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)Electron microscopy3.42018-11-21
136MTC|1|5+ 6MTC|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)Electron microscopy3.42018-11-21
146GZ5|1|A2+ 6GZ5|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)Electron microscopy3.52018-12-05
155LZZ|1|5+ 5LZZ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)Electron microscopy3.472016-11-30
166GZ3|1|A2+ 6GZ3|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)Electron microscopy3.62018-12-05
175LZW|1|5+ 5LZW|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a truncated mRNA.Electron microscopy3.532016-11-30
185LZX|1|5+ 5LZX|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a UGA stop codon.Electron microscopy3.672016-11-30
196GZ4|1|A2+ 6GZ4|1|A3Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)Electron microscopy3.62018-12-05
205LZT|1|5+ 5LZT|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.Electron microscopy3.652016-11-30
211VX0|1|5+ 1VX0|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the translating mammalian ribosome-Sec61 complex. This entry contains the large subunit ribosomal RNA.Electron microscopy3.92014-06-18
223J73|1|5+ 3J73|1|828S ribosomal RNA, 5.8S ribosomal RNAStructure of the translating mammalian ribosome-Sec61 complexElectron microscopy3.92014-06-18
236MTB|1|5+ 6MTB|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)Electron microscopy3.62018-11-21
246HCJ|1|51+ 6HCJ|1|81Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAsElectron microscopy3.82018-10-17
255LZU|1|5+ 5LZU|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian ribosomal termination complex with accommodated eRF1Electron microscopy3.752016-11-30
266FRK|1|5+ 6FRK|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complexElectron microscopy3.72018-03-28
276HCF|1|52+ 6HCF|1|82Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the rabbit 80S ribosome stalled on globin mRNA at the stop codonElectron microscopy3.92018-10-17
283JAH|1|5+ 3JAH|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonElectron microscopy3.452015-08-12
295LZY|1|5+ 5LZY|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.Electron microscopy3.992016-11-30
303JAG|1|5+ 3JAG|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codonElectron microscopy3.652015-08-12
313JAI|1|5+ 3JAI|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codonElectron microscopy3.652015-08-12
323J92|1|5+ 3J92|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S rRNA, 5.8S rRNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure and assembly pathway of the ribosome quality control complexElectron microscopy3.62015-01-21
333JAN|1|5+ 3JAN|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the scanning state of the mammalian SRP-ribosome complexElectron microscopy3.752015-08-05
343JAJ|1|5+ 3JAJ|1|8Large subunit ribosomal RNA + 5.8S ribosomal RNA28S ribosomal RNA, 5.8S ribosomal RNAOryctolagus cuniculusEukaryaRF02543 + RF00002Structure of the engaged state of the mammalian SRP-ribosome complexElectron microscopy3.752015-08-05

Release history

Release3.513.523.533.543.553.563.573.583.593.603.613.623.633.643.653.663.673.683.693.703.713.723.733.743.753.763.773.783.793.803.81
Date2018-12-072018-12-142018-12-212018-12-282019-01-042019-01-112019-01-182019-01-252019-02-012019-02-082019-02-152019-02-222019-03-012019-03-082019-03-152019-03-222019-03-292019-04-052019-04-122019-04-192019-04-262019-05-032019-05-102019-05-172019-05-242019-05-312019-06-072019-06-142019-06-212019-06-282019-07-05

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_4.0_06650.8NR_4.0_06650.73.51(31) 5LZY|1|5+5LZY|1|8, 6MTE|1|5+6MTE|1|8, 3JAG|1|5+3JAG|1|8, 5LZX|1|5+5LZX|1|8, 3J92|1|5+3J92|1|8, 6MTD|1|5+6MTD|1|8, 5LZW|1|5+5LZW|1|8, 3J74|1|5+3J74|1|8, 6MTC|1|5+6MTC|1|8, 5LZV|1|5+5LZV|1|8, 3J73|1|5+3J73|1|8, 6MTB|1|5+6MTB|1|8, 5LZU|1|5+5LZU|1|8, 3J72|1|5+3J72|1|8, 6HCJ|1|51+6HCJ|1|81, 5LZT|1|5+5LZT|1|8, 3J71|1|5+3J71|1|8, 6HCF|1|52+6HCF|1|82, 5LZS|1|5+5LZS|1|8, 1VX3|1|5+1VX3|1|8, 6FRK|1|5+6FRK|1|8, 3JAN|1|5+3JAN|1|8, 1VX0|1|5+1VX0|1|8, 6D9J|1|5+6D9J|1|8, 3JAJ|1|5+3JAJ|1|8, 1VWY|1|5+1VWY|1|8, 6D90|1|5+6D90|1|8, 3JAI|1|5+3JAI|1|8, 1VWW|1|5+1VWW|1|8, 5LZZ|1|5+5LZZ|1|8, 3JAH|1|5+3JAH|1|8(3) 6GZ3|1|A2+6GZ3|1|A3, 6GZ5|1|A2+6GZ5|1|A3, 6GZ4|1|A2+6GZ4|1|A3(0)

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
16HCJ|1|51+6HCJ|1|81Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAsELECTRON MICROSCOPY3.83635
25LZY|1|5+5LZY|1|8Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.ELECTRON MICROSCOPY3.993543
35LZZ|1|5+5LZZ|1|8Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)ELECTRON MICROSCOPY3.473543
45LZX|1|5+5LZX|1|8Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a UGA stop codon.ELECTRON MICROSCOPY3.673543
55LZW|1|5+5LZW|1|8Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a truncated mRNA.ELECTRON MICROSCOPY3.533543
65LZT|1|5+5LZT|1|8Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.ELECTRON MICROSCOPY3.653543
75LZS|1|5+5LZS|1|8Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BELECTRON MICROSCOPY3.313543
85LZU|1|5+5LZU|1|8Structure of the mammalian ribosomal termination complex with accommodated eRF1ELECTRON MICROSCOPY3.753543
95LZV|1|5+5LZV|1|8Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.ELECTRON MICROSCOPY3.353543
106MTC|1|5+6MTC|1|8Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)ELECTRON MICROSCOPY3.43497
116MTB|1|5+6MTB|1|8Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)ELECTRON MICROSCOPY3.63497
126MTD|1|5+6MTD|1|8Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)ELECTRON MICROSCOPY3.33497
136MTE|1|5+6MTE|1|8Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)ELECTRON MICROSCOPY3.43497
146HCF|1|52+6HCF|1|82Structure of the rabbit 80S ribosome stalled on globin mRNA at the stop codonELECTRON MICROSCOPY3.93634
156D90|1|5+6D90|1|8Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.ELECTRON MICROSCOPY3.23594
166D9J|1|5+6D9J|1|8Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.ELECTRON MICROSCOPY3.23594
171VWY|1|5+1VWY|1|8Structure of the idle mammalian ribosome-Sec61 complex. This entry contains the large subunit ribosomal RNA.ELECTRON MICROSCOPY3.43662
181VWW|1|5+1VWW|1|8Structure of the mammalian 60S ribosomal subunit. This entry contains the large subunit ribosomal RNA.ELECTRON MICROSCOPY3.43662
193J71|1|5+3J71|1|8Structure of the mammalian 60S ribosomal subunitELECTRON MICROSCOPY3.43662
203J74|1|5+3J74|1|8Structure of the 80S mammalian ribosome bound to eEF2ELECTRON MICROSCOPY3.53662
211VX3|1|5+1VX3|1|8Structure of the 80S mammalian ribosome bound to eEF2. This entry contains the large subunit ribosomal RNA.ELECTRON MICROSCOPY3.53662
223J72|1|5+3J72|1|8Structure of the idle mammalian ribosome-Sec61 complexELECTRON MICROSCOPY3.43662
233J73|1|5+3J73|1|8Structure of the translating mammalian ribosome-Sec61 complexELECTRON MICROSCOPY3.93720
241VX0|1|5+1VX0|1|8Structure of the translating mammalian ribosome-Sec61 complex. This entry contains the large subunit ribosomal RNA.ELECTRON MICROSCOPY3.93720
253J92|1|5+3J92|1|8Structure and assembly pathway of the ribosome quality control complexELECTRON MICROSCOPY3.63662
266FRK|1|5+6FRK|1|8Structure of a prehandover mammalian ribosomal SRP and SRP receptor targeting complexELECTRON MICROSCOPY3.73658
273JAJ|1|5+3JAJ|1|8Structure of the engaged state of the mammalian SRP-ribosome complexELECTRON MICROSCOPY3.753658
283JAN|1|5+3JAN|1|8Structure of the scanning state of the mammalian SRP-ribosome complexELECTRON MICROSCOPY3.753658
293JAG|1|5+3JAG|1|8Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codonELECTRON MICROSCOPY3.653662
303JAH|1|5+3JAH|1|8Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonELECTRON MICROSCOPY3.453662
313JAI|1|5+3JAI|1|8Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codonELECTRON MICROSCOPY3.653662
326GZ4|1|A2+6GZ4|1|A3tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)ELECTRON MICROSCOPY3.63612
336GZ3|1|A2+6GZ3|1|A3tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)ELECTRON MICROSCOPY3.63612
346GZ5|1|A2+6GZ5|1|A3tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.53612
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