RNA 3D Hub //

Equivalence class NR_20.0_69141.4 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. ÅDate
19CBX|1|N (rep)Group I catalytic intronRNA (387-MER)Tetrahymena thermophilaEukaryaRF00028Tetrahymena ribozyme with automatically identified water and magnesium ionsElectron microscopy2.22024-11-20
29CBU|1|NGroup I catalytic intronRNA (387-MER)Tetrahymena thermophilaEukaryaRF00028Tetrahymena ribozyme with consensus water and magnesium ionsElectron microscopy2.22024-11-20
39CBY|1|NGroup I catalytic intronRNA (387-MER)Tetrahymena thermophilaEukaryaRF00028Tetrahymena ribozyme with automatically identified water and magnesium ionsElectron microscopy2.32024-11-20
49CBW|1|NGroup I catalytic intronRNA (387-MER)Tetrahymena thermophilaEukaryaRF00028Tetrahymena ribozyme with consensus water and magnesium ionsElectron microscopy2.32024-11-20
57YGA|1|NGroup I catalytic intronRNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*U)-3'), RNA (5'-R(*UP*CP*GP*(SSU)P*AP*AP*CP*C)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicingElectron microscopy2.352023-03-29
67XD6|1|NGroup I catalytic intronThe Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon), The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)Tetrahymena thermophilaEukaryaRF00028The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonElectron microscopy2.842023-04-05
77YGB|1|NGroup I catalytic intronRNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the second-step self-splicingElectron microscopy2.622023-03-29
88I7N|1|NThe Tet-S1 state molecule of co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideTetrahymena thermophilaThe Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideElectron microscopy2.982023-03-29
97YGC|1|NGroup I catalytic intronRNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicingElectron microscopy2.652023-03-29
107XD5|1|NGroup I catalytic intronThe Tet-S2 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon), The Tet-S2 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)Tetrahymena thermophilaEukaryaRF00028The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonElectron microscopy2.842023-04-05
117YG9|1|NGroup I catalytic intronRNA (391-MER), RNA (5'-R(*CP*CP*CP*UP*CP*U)-3'), RNA (5'-R(*UP*CP*GP*(SSU)P*AP*AP*C)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the second-step self-splicingElectron microscopy2.682023-03-29
127XD7|1|NGroup I catalytic intronThe pre-Tet-C state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exonTetrahymena thermophilaEukaryaRF00028The pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonElectron microscopy3.022023-03-29
137EZ2|1|NGroup I catalytic intronHolo L-16 ScaI Tetrahymena ribozyme, Holo L-16 ScaI Tetrahymena ribozyme S1, Holo L-16 ScaI Tetrahymena ribozyme S2Tetrahymena thermophilaEukaryaRF00028Holo L-16 ScaI Tetrahymena ribozymeElectron microscopy3.052021-08-25
147XSN|1|NGroup I catalytic intronRNA (387-MER)Tetrahymena thermophilaEukaryaRF00028Native Tetrahymena ribozyme conformationElectron microscopy3.012022-08-03
157YG8|1|NGroup I catalytic intronRNA (387-MER), RNA (5'-R(*CP*CP*CP*UP*C)-3'), RNA (5'-R(*UP*CP*G)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicingElectron microscopy2.972023-03-29
167YCI|1|NGroup I catalytic intronRNA (389-MER), RNA (5'-R(*CP*CP*CP*UP*CP*U)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicingElectron microscopy2.982023-07-05
177EZ0|1|NGroup I catalytic intronApo L-21 ScaI Tetrahymena ribozymeTetrahymena thermophilaEukaryaRF00028Apo L-21 ScaI Tetrahymena ribozymeElectron microscopy3.142021-08-25
187YCH|1|NGroup I catalytic intronRNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicingElectron microscopy3.092023-07-05
197R6L|1|AGroup I catalytic intronGroup I intron, 3 prime fragment plus 3 prime exon, Group I intron, 5 prime fragmentTetrahymena thermophilaEukaryaRF000285 prime exon-free pre-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric constructElectron microscopy2.852022-05-04
208HD7|1|NThe intermediate pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideTetrahymena thermophilaThe intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideElectron microscopy3.522023-03-29
217YCG|1|NGroup I catalytic intronRNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicingElectron microscopy3.182023-07-05
228HD6|1|NThe relaxed pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideTetrahymena thermophilaThe relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideElectron microscopy3.732023-03-29
237YGD|1|NGroup I catalytic intronRNA (384-MER), RNA (5'-R(*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3')TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicingElectron microscopy3.412023-03-29
247XD4|1|NGroup I catalytic intronCo-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exonTetrahymena thermophilaEukaryaRF00028The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exonElectron microscopy3.892023-03-29
257XD3|1|NGroup I catalytic intronThe relaxed pre-Tet-S1 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exonTetrahymena thermophilaEukaryaRF00028The relaxed pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exonElectron microscopy4.052023-03-29
267XSK|1|NGroup I catalytic intronRNA (388-MER)Tetrahymena thermophilaEukaryaRF00028Misfolded Tetrahymena ribozyme conformation 1Electron microscopy3.532022-08-03
277R6M|1|AGroup I catalytic intronGroup I intron, Ligated exon mimic of the Group I intronTetrahymena thermophilaEukaryaRF00028Post-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric constructElectron microscopy3.682022-05-04
287UVT|1|AGroup I catalytic intronRNA (386-MER)Tetrahymena thermophilaEukaryaRF00028Kinetically trapped misfolded state of the Tetrahymena ribozymeElectron microscopy3.92022-08-31
297XSL|1|NGroup I catalytic intronRNA (388-MER)Tetrahymena thermophilaEukaryaRF00028Misfolded Tetrahymena ribozyme conformation 2Electron microscopy3.842022-08-03
307XSM|1|NGroup I catalytic intronRNA (388-MER)Tetrahymena thermophilaEukaryaRF00028Misfolded Tetrahymena ribozyme conformation 3Electron microscopy4.012022-08-03
317R6N|1|AGroup I catalytic intronGroup I intronTetrahymena thermophilaEukaryaRF00028Exon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric constructElectron microscopy4.12022-05-04
327YC8|1|NGroup I catalytic intronRNA (388-MER)TetrahymenaEukaryaRF00028Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicingElectron microscopy4.142023-07-05
336WLS|11|AGroup I catalytic intronRNA (388-MER)Tetrahymena thermophilaEukaryaRF00028Tetrahymena ribozyme models, 6.8 Angstrom resolutionElectron microscopy6.82020-07-08

Release history

Release3.3623.3633.3643.3653.3663.3673.3683.3693.3703.3713.372
Date2024-11-202024-11-272024-12-042024-12-112024-12-182024-12-252025-01-012025-01-082025-01-152025-01-222025-01-29

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

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.

#SViewPDBTitleMethodResolutionLength
17XSL|1|NMisfolded Tetrahymena ribozyme conformation 2ELECTRON MICROSCOPY3.84388
27XSM|1|NMisfolded Tetrahymena ribozyme conformation 3ELECTRON MICROSCOPY4.01388
37XSK|1|NMisfolded Tetrahymena ribozyme conformation 1ELECTRON MICROSCOPY3.53388
47UVT|1|AKinetically trapped misfolded state of the Tetrahymena ribozymeELECTRON MICROSCOPY3.9386
56WLS|11|ATetrahymena ribozyme models, 6.8 Angstrom resolutionELECTRON MICROSCOPY6.8388
68HD6|1|NThe relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideELECTRON MICROSCOPY3.73419
77XD3|1|NThe relaxed pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exonELECTRON MICROSCOPY4.05423
87YC8|1|NCryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the first-step self-splicingELECTRON MICROSCOPY4.14388
97YCG|1|NCryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicingELECTRON MICROSCOPY3.18393
107YGC|1|NCryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicingELECTRON MICROSCOPY2.65393
117YG8|1|NCryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicingELECTRON MICROSCOPY2.97387
127YGD|1|NCryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicingELECTRON MICROSCOPY3.41384
139CBW|1|NTetrahymena ribozyme with consensus water and magnesium ionsELECTRON MICROSCOPY2.3387
149CBY|1|NTetrahymena ribozyme with automatically identified water and magnesium ionsELECTRON MICROSCOPY2.3387
157XSN|1|NNative Tetrahymena ribozyme conformationELECTRON MICROSCOPY3.01387
169CBX|1|NTetrahymena ribozyme with automatically identified water and magnesium ionsELECTRON MICROSCOPY2.2387
179CBU|1|NTetrahymena ribozyme with consensus water and magnesium ionsELECTRON MICROSCOPY2.2387
187EZ0|1|NApo L-21 ScaI Tetrahymena ribozymeELECTRON MICROSCOPY3.14387
197XD7|1|NThe pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonELECTRON MICROSCOPY3.02405
207R6N|1|AExon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric constructELECTRON MICROSCOPY4.1354
217XD4|1|NThe intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exonELECTRON MICROSCOPY3.89423
228HD7|1|NThe intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideELECTRON MICROSCOPY3.52419
237XD5|1|NThe Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonELECTRON MICROSCOPY2.84400
248I7N|1|NThe Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleosideELECTRON MICROSCOPY2.98418
257EZ2|1|NHolo L-16 ScaI Tetrahymena ribozymeELECTRON MICROSCOPY3.05392
267XD6|1|NThe Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exonELECTRON MICROSCOPY2.84434
277YG9|1|NCryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the second-step self-splicingELECTRON MICROSCOPY2.68391
287YGA|1|NCryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicingELECTRON MICROSCOPY2.35393
297YGB|1|NCryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the second-step self-splicingELECTRON MICROSCOPY2.62393
307YCI|1|NCryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the first-step self-splicingELECTRON MICROSCOPY2.98389
317YCH|1|NCryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the first-step self-splicingELECTRON MICROSCOPY3.09393
327R6M|1|APost-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric constructELECTRON MICROSCOPY3.68356
337R6L|1|A5 prime exon-free pre-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric constructELECTRON MICROSCOPY2.85343

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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