RNA 3D Hub //

Equivalence class NR_4.0_21280.12 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
16SGC|1|A1 (rep)Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome stalled on a poly(A) tailElectron microscopy2.82019-12-04
26YAL|1|2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Mammalian 48S late-stage initiation complex with beta-globin mRNAElectron microscopy32020-04-08
36R5Q|1|KSmall subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of XBP1u-paused ribosome nascent chain complex (post-state)Electron microscopy32019-07-10
46P5I|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)Electron microscopy3.12019-09-18
56P5K|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)Electron microscopy3.12019-09-18
66P5J|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)Electron microscopy3.12019-09-18
76P4G|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)Electron microscopy3.12019-09-18
86R6P|1|KSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of XBP1u-paused ribosome nascent chain complex (rotated state)Electron microscopy3.12019-07-10
96P4H|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)Electron microscopy3.22019-09-18
106P5N|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1Electron microscopy3.22019-09-25
116D9J|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.Electron microscopy3.22018-06-06
125LZS|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BElectron microscopy3.312016-11-30
136W2T|1|aSmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)Electron microscopy3.362020-04-22
141VX5|1|218S ribosomal RNAStructure of the 80S mammalian ribosome bound to eEF2. This entry contains the small ribosomal subunit.Electron microscopy3.52014-06-18
153J74|1|S218S ribosomal RNAStructure of the 80S mammalian ribosome bound to eEF2Electron microscopy3.52014-06-18
166MTD|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)Electron microscopy3.32018-11-21
175LZV|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.Electron microscopy3.352016-11-30
186D90|1|2Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.Electron microscopy3.22018-06-06
196YAN|1|2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Mammalian 48S late-stage translation initiation complex with histone 4 mRNAElectron microscopy3.482020-04-08
206MTC|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)Electron microscopy3.42018-11-21
216MTE|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)Electron microscopy3.42018-11-21
226W2S|1|ASmall subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)Electron microscopy3.472020-04-22
236GZ5|1|B1Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)Electron microscopy3.52018-12-05
245LZZ|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)Electron microscopy3.472016-11-30
255LZW|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a truncated mRNA.Electron microscopy3.532016-11-30
265LZX|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a UGA stop codon.Electron microscopy3.672016-11-30
276GZ3|1|B1Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)Electron microscopy3.62018-12-05
286GZ4|1|B1Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)Electron microscopy3.62018-12-05
295LZT|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.Electron microscopy3.652016-11-30
306YAM|1|2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNAElectron microscopy3.62020-04-08
316MTB|1|9Small subunit ribosomal RNA18S rRNAOryctolagus cuniculusEukaryaRF01960Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)Electron microscopy3.62018-11-21
326HCJ|1|A2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAsElectron microscopy3.82018-10-17
331VX2|1|218S ribosomal RNAStructure of the translating mammalian ribosome-Sec61 complex. This entry contains the small ribosomal subunit.Electron microscopy3.92014-06-18
343J73|1|S218S ribosomal RNAStructure of the translating mammalian ribosome-Sec61 complexElectron microscopy3.92014-06-18
356R6G|1|KSmall subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of XBP1u-paused ribosome nascent chain complex with SRP.Electron microscopy3.72019-07-10
365LZU|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian ribosomal termination complex with accommodated eRF1Electron microscopy3.752016-11-30
376HCF|1|A1Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the rabbit 80S ribosome stalled on globin mRNA at the stop codonElectron microscopy3.92018-10-17
386R7Q|1|KSmall subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of XBP1u-paused ribosome nascent chain complex with Sec61.Electron microscopy3.92019-07-10
393JAH|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonElectron microscopy3.452015-08-12
405LZY|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.Electron microscopy3.992016-11-30
415FLX|1|1Small subunit ribosomal RNA18S RRNAOryctolagus cuniculusEukaryaRF01960Mammalian 40S HCV-IRES complexElectron microscopy3.92015-12-23
423JAG|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codonElectron microscopy3.652015-08-12
433JAI|1|9Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codonElectron microscopy3.652015-08-12
443JAN|1|S2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the scanning state of the mammalian SRP-ribosome complexElectron microscopy3.752015-08-05
453JAJ|1|S2Small subunit ribosomal RNA18S ribosomal RNAOryctolagus cuniculusEukaryaRF01960Structure of the engaged state of the mammalian SRP-ribosome complexElectron microscopy3.752015-08-05

Release history

Release3.1233.1243.1253.1263.1273.1283.1293.1303.1313.1323.1333.1343.1353.1363.1373.1383.139
Date2020-04-222020-04-292020-05-062020-05-132020-05-202020-05-272020-06-032020-06-102020-06-172020-06-242020-07-012020-07-082020-07-152020-07-222020-07-292020-08-052020-08-12

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent
NR_4.0_21280.12NR_4.0_21280.113.123(43) 1VX5|1|2, 5LZZ|1|9, 6P5K|1|2, 1VX2|1|2, 5LZY|1|9, 6P5J|1|2, 5LZX|1|9, 6P5I|1|2, 5LZW|1|9, 6P4H|1|2, 5LZV|1|9, 6P4G|1|2, 5LZU|1|9, 6MTE|1|9, 5LZT|1|9, 6MTD|1|9, 5LZS|1|9, 6MTC|1|9, 6YAN|1|2, 5FLX|1|1, 6MTB|1|9, 6YAM|1|2, 3JAN|1|S2, 6HCJ|1|A2, 6YAL|1|2, 3JAJ|1|S2, 6HCF|1|A1, 6SGC|1|A1, 3JAI|1|9, 6GZ5|1|B1, 6R7Q|1|K, 3JAH|1|9, 6GZ4|1|B1, 6R6P|1|K, 3JAG|1|9, 6GZ3|1|B1, 6R6G|1|K, 3J74|1|S2, 6D9J|1|2, 6R5Q|1|K, 3J73|1|S2, 6D90|1|2, 6P5N|1|2(2) 6W2S|1|A, 6W2T|1|a(0)

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child
NR_4.0_21280.12NR_4.0_21280.133.140(41) 6R7Q|1|K, 6SGC|1|A1, 6W2S|1|A, 6W2T|1|a, 6YAL|1|2, 6YAM|1|2, 6YAN|1|2, 6GZ4|1|B1, 3JAG|1|9, 6GZ5|1|B1, 3JAH|1|9, 6HCF|1|A1, 3JAI|1|9, 6HCJ|1|A2, 3JAJ|1|S2, 6MTB|1|9, 3JAN|1|S2, 6MTC|1|9, 5FLX|1|1, 6MTD|1|9, 5LZS|1|9, 6MTE|1|9, 5LZT|1|9, 6P4G|1|2, 5LZU|1|9, 6P4H|1|2, 5LZV|1|9, 6P5I|1|2, 5LZW|1|9, 6P5J|1|2, 5LZX|1|9, 6P5K|1|2, 5LZY|1|9, 6P5N|1|2, 5LZZ|1|9, 6R5Q|1|K, 6D90|1|2, 6R6G|1|K, 6D9J|1|2, 6GZ3|1|B1, 6R6P|1|K(4) 1VX2|1|2, 3J74|1|S2, 3J73|1|S2, 1VX5|1|2(0)
NR_4.0_21280.12NR_4.0_46995.133.140(4) 3J74|1|S2, 1VX5|1|2, 1VX2|1|2, 3J73|1|S2(41) 6R6P|1|K, 6SGC|1|A1, 6YAN|1|2, 5LZU|1|9, 5LZX|1|9, 6P4G|1|2, 6P5I|1|2, 3JAG|1|9, 3JAJ|1|S2, 6GZ4|1|B1, 6HCF|1|A1, 6W2S|1|A, 6YAM|1|2, 5LZV|1|9, 5LZY|1|9, 6P5J|1|2, 6R5Q|1|K, 3JAN|1|S2, 5LZS|1|9, 6HCJ|1|A2, 6MTD|1|9, 6W2T|1|a, 6D9J|1|2, 6P5K|1|2, 5LZT|1|9, 6MTB|1|9, 3JAI|1|9, 5LZZ|1|9, 6GZ3|1|B1, 6R6G|1|K, 5FLX|1|1, 5LZW|1|9, 6MTE|1|9, 6D90|1|2, 3JAH|1|9, 6GZ5|1|B1, 6P4H|1|2, 6YAL|1|2, 6P5N|1|2, 6MTC|1|9, 6R7Q|1|K(40) 6G5H|1|2, 6OLE|1|S2, 4UG0|1|S2, 6IP8|1|2m, 6ZP4|1|2, 6ZOL|1|2, 6ZVH|1|2, 6Z6M|1|S2, 6Y57|1|S2, 6ZLW|1|2, 6IP5|1|2m, 6ZON|1|2, 6G5I|1|2, 6OLF|1|S2, 6Z6L|1|S2, 5A2Q|1|2, 6Z6N|1|S2, 6ZOK|1|2, 6ZM7|1|S2, 6Y2L|1|S2, 6OLG|1|B1, 5A8L|1|B, 5LKS|1|S2, 6ZMI|1|S2, 6OLZ|1|B1, 5AJ0|1|B1, 6ZME|1|S2, 6OLI|1|S2, 6ZMO|1|S2, 6OM0|1|S2, 5T2C|1|AA, 6OM7|1|S2, 6G18|1|2, 6ZN5|1|2, 6ZMT|1|2, 6QZP|1|S2, 6ZOJ|1|2, 6EK0|1|S2, 6Y0G|1|S2, 6G4S|1|2

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
13J73|1|S2Structure of the translating mammalian ribosome-Sec61 complexELECTRON MICROSCOPY3.91742
21VX2|1|2Structure of the translating mammalian ribosome-Sec61 complex. This entry contains the small ribosomal subunit.ELECTRON MICROSCOPY3.91742
36YAN|1|2Mammalian 48S late-stage translation initiation complex with histone 4 mRNAELECTRON MICROSCOPY3.481743
46YAL|1|2Mammalian 48S late-stage initiation complex with beta-globin mRNAELECTRON MICROSCOPY31743
56YAM|1|2Mammalian 48S late-stage translation initiation complex (LS48S+eIF3 IC) with beta-globin mRNAELECTRON MICROSCOPY3.61742
63JAJ|1|S2Structure of the engaged state of the mammalian SRP-ribosome complexELECTRON MICROSCOPY3.751742
73JAN|1|S2Structure of the scanning state of the mammalian SRP-ribosome complexELECTRON MICROSCOPY3.751742
83JAH|1|9Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codonELECTRON MICROSCOPY3.451719
93JAG|1|9Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAA stop codonELECTRON MICROSCOPY3.651719
103JAI|1|9Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UGA stop codonELECTRON MICROSCOPY3.651719
116GZ5|1|B1tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3)ELECTRON MICROSCOPY3.51708
126HCJ|1|A2Structure of the rabbit 80S ribosome on globin mRNA in the rotated state with A/P and P/E tRNAsELECTRON MICROSCOPY3.81740
136HCF|1|A1Structure of the rabbit 80S ribosome stalled on globin mRNA at the stop codonELECTRON MICROSCOPY3.91732
146D90|1|2Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.ELECTRON MICROSCOPY3.21697
156P5N|1|2Structure of a mammalian 80S ribosome in complex with a single translocated Israeli Acute Paralysis Virus IRES and eRF1ELECTRON MICROSCOPY3.21697
166SGC|1|A1Rabbit 80S ribosome stalled on a poly(A) tailELECTRON MICROSCOPY2.81697
175LZW|1|9Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a truncated mRNA.ELECTRON MICROSCOPY3.531698
185LZX|1|9Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a UGA stop codon.ELECTRON MICROSCOPY3.671698
195LZZ|1|9Structure of the mammalian rescue complex with Pelota and Hbs1l (combined)ELECTRON MICROSCOPY3.471698
205LZY|1|9Structure of the mammalian rescue complex with Pelota and Hbs1l assembled on a polyadenylated mRNA.ELECTRON MICROSCOPY3.991698
215LZU|1|9Structure of the mammalian ribosomal termination complex with accommodated eRF1ELECTRON MICROSCOPY3.751698
225LZV|1|9Structure of the mammalian ribosomal termination complex with accommodated eRF1(AAQ) and ABCE1.ELECTRON MICROSCOPY3.351698
235LZT|1|9Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.ELECTRON MICROSCOPY3.651698
245LZS|1|9Structure of the mammalian ribosomal elongation complex with aminoacyl-tRNA, eEF1A, and didemnin BELECTRON MICROSCOPY3.311697
256MTB|1|9Rabbit 80S ribosome with P- and Z-site tRNAs (unrotated state)ELECTRON MICROSCOPY3.61664
266MTC|1|9Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state)ELECTRON MICROSCOPY3.41664
276R7Q|1|KStructure of XBP1u-paused ribosome nascent chain complex with Sec61.ELECTRON MICROSCOPY3.91698
286R5Q|1|KStructure of XBP1u-paused ribosome nascent chain complex (post-state)ELECTRON MICROSCOPY31698
296R6G|1|KStructure of XBP1u-paused ribosome nascent chain complex with SRP.ELECTRON MICROSCOPY3.71698
306R6P|1|KStructure of XBP1u-paused ribosome nascent chain complex (rotated state)ELECTRON MICROSCOPY3.11698
316P4H|1|2Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 2)ELECTRON MICROSCOPY3.21697
326P4G|1|2Structure of a mammalian small ribosomal subunit in complex with the Israeli Acute Paralysis Virus IRES (Class 1)ELECTRON MICROSCOPY3.11697
336P5K|1|2Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 3)ELECTRON MICROSCOPY3.11697
346P5I|1|2Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 1)ELECTRON MICROSCOPY3.11697
356P5J|1|2Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)ELECTRON MICROSCOPY3.11697
366MTE|1|9Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)ELECTRON MICROSCOPY3.41664
376MTD|1|9Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel)ELECTRON MICROSCOPY3.31692
386GZ4|1|B1tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-2 (TI-POST-2)ELECTRON MICROSCOPY3.61708
396GZ3|1|B1tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)ELECTRON MICROSCOPY3.61708
405FLX|1|1Mammalian 40S HCV-IRES complexELECTRON MICROSCOPY3.91708
416W2T|1|aStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)ELECTRON MICROSCOPY3.361697
426W2S|1|AStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)ELECTRON MICROSCOPY3.471697
436D9J|1|2Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1.ELECTRON MICROSCOPY3.21697
441VX5|1|2Structure of the 80S mammalian ribosome bound to eEF2. This entry contains the small ribosomal subunit.ELECTRON MICROSCOPY3.51742
453J74|1|S2Structure of the 80S mammalian ribosome bound to eEF2ELECTRON MICROSCOPY3.51742
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