Equivalence class NR_20.0_69141.2 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7YGA|1|N (rep) | Group I catalytic intron | RNA (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') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicing | Electron microscopy | 2.35 | 2023-03-29 |
| 2 | 7XD6|1|N | Group I catalytic intron | 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 (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 thermophila | Eukarya | RF00028 | The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | Electron microscopy | 2.84 | 2023-04-05 |
| 3 | 7YGB|1|N | Group I catalytic intron | RNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the second-step self-splicing | Electron microscopy | 2.62 | 2023-03-29 |
| 4 | 8I7N|1|N | The Tet-S1 state molecule of co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Tetrahymena thermophila | The Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Electron microscopy | 2.98 | 2023-03-29 | |||
| 5 | 7YGC|1|N | Group I catalytic intron | RNA (393-MER), RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing | Electron microscopy | 2.65 | 2023-03-29 |
| 6 | 7XD5|1|N | Group I catalytic intron | The 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 thermophila | Eukarya | RF00028 | The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | Electron microscopy | 2.84 | 2023-04-05 |
| 7 | 7YG9|1|N | Group I catalytic intron | RNA (391-MER), RNA (5'-R(*CP*CP*CP*UP*CP*U)-3'), RNA (5'-R(*UP*CP*GP*(SSU)P*AP*AP*C)-3') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the second-step self-splicing | Electron microscopy | 2.68 | 2023-03-29 |
| 8 | 7XD7|1|N | Group I catalytic intron | The pre-Tet-C state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | Tetrahymena thermophila | Eukarya | RF00028 | The pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | Electron microscopy | 3.02 | 2023-03-29 |
| 9 | 7EZ2|1|N | Group I catalytic intron | Holo L-16 ScaI Tetrahymena ribozyme, Holo L-16 ScaI Tetrahymena ribozyme S1, Holo L-16 ScaI Tetrahymena ribozyme S2 | Tetrahymena thermophila | Eukarya | RF00028 | Holo L-16 ScaI Tetrahymena ribozyme | Electron microscopy | 3.05 | 2021-08-25 |
| 10 | 7XSN|1|N | Group I catalytic intron | RNA (387-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Native Tetrahymena ribozyme conformation | Electron microscopy | 3.01 | 2022-08-03 |
| 11 | 7YG8|1|N | Group I catalytic intron | RNA (387-MER), RNA (5'-R(*CP*CP*CP*UP*C)-3'), RNA (5'-R(*UP*CP*G)-3') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing | Electron microscopy | 2.97 | 2023-03-29 |
| 12 | 7EZ0|1|N | Group I catalytic intron | Apo L-21 ScaI Tetrahymena ribozyme | Tetrahymena thermophila | Eukarya | RF00028 | Apo L-21 ScaI Tetrahymena ribozyme | Electron microscopy | 3.14 | 2021-08-25 |
| 13 | 7R6L|1|A | Group I catalytic intron | Group I intron, 3 prime fragment plus 3 prime exon, Group I intron, 5 prime fragment | Tetrahymena thermophila | Eukarya | RF00028 | 5 prime exon-free pre-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | Electron microscopy | 2.85 | 2022-05-04 |
| 14 | 8HD7|1|N | The intermediate pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Tetrahymena thermophila | The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Electron microscopy | 3.52 | 2023-03-29 | |||
| 15 | 8HD6|1|N | The relaxed pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Tetrahymena thermophila | The relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | Electron microscopy | 3.73 | 2023-03-29 | |||
| 16 | 7YGD|1|N | Group I catalytic intron | RNA (384-MER), RNA (5'-R(*CP*C)-3'), RNA (5'-R(*UP*CP*G)-3') | Tetrahymena | Eukarya | RF00028 | Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing | Electron microscopy | 3.41 | 2023-03-29 |
| 17 | 7XD4|1|N | Group I catalytic intron | Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | Tetrahymena thermophila | Eukarya | RF00028 | The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | Electron microscopy | 3.89 | 2023-03-29 |
| 18 | 7XD3|1|N | Group I catalytic intron | The relaxed pre-Tet-S1 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | Tetrahymena thermophila | Eukarya | RF00028 | The relaxed pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | Electron microscopy | 4.05 | 2023-03-29 |
| 19 | 7XSK|1|N | Group I catalytic intron | RNA (388-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Misfolded Tetrahymena ribozyme conformation 1 | Electron microscopy | 3.53 | 2022-08-03 |
| 20 | 7R6M|1|A | Group I catalytic intron | Group I intron, Ligated exon mimic of the Group I intron | Tetrahymena thermophila | Eukarya | RF00028 | Post-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | Electron microscopy | 3.68 | 2022-05-04 |
| 21 | 7UVT|1|A | Group I catalytic intron | RNA (386-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Kinetically trapped misfolded state of the Tetrahymena ribozyme | Electron microscopy | 3.9 | 2022-08-31 |
| 22 | 7XSL|1|N | Group I catalytic intron | RNA (388-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Misfolded Tetrahymena ribozyme conformation 2 | Electron microscopy | 3.84 | 2022-08-03 |
| 23 | 7XSM|1|N | Group I catalytic intron | RNA (388-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Misfolded Tetrahymena ribozyme conformation 3 | Electron microscopy | 4.01 | 2022-08-03 |
| 24 | 7R6N|1|A | Group I catalytic intron | Group I intron | Tetrahymena thermophila | Eukarya | RF00028 | Exon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | Electron microscopy | 4.1 | 2022-05-04 |
| 25 | 6WLS|11|A | Group I catalytic intron | RNA (388-MER) | Tetrahymena thermophila | Eukarya | RF00028 | Tetrahymena ribozyme models, 6.8 Angstrom resolution | Electron microscopy | 6.8 | 2020-07-08 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_20.0_69141.2 | NR_20.0_69141.1 | 3.277 | (23) 6WLS|11|A, 7EZ0|1|N, 7EZ2|1|N, 7R6L|1|A, 7R6M|1|A, 7R6N|1|A, 7UVT|1|A, 7XD3|1|N, 7XD4|1|N, 7XD7|1|N, 7XSK|1|N, 7XSL|1|N, 7XSM|1|N, 7XSN|1|N, 7YG8|1|N, 7YG9|1|N, 7YGA|1|N, 7YGB|1|N, 7YGC|1|N, 7YGD|1|N, 8HD6|1|N, 8HD7|1|N, 8I7N|1|N | (2) 7XD5|1|N, 7XD6|1|N | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_20.0_69141.2 | NR_20.0_69141.3 | 3.290 | (25) 6WLS|11|A, 7EZ0|1|N, 7EZ2|1|N, 7R6L|1|A, 7R6M|1|A, 7R6N|1|A, 7UVT|1|A, 7XD3|1|N, 7XD4|1|N, 7XD5|1|N, 7XD6|1|N, 7XD7|1|N, 7XSK|1|N, 7XSL|1|N, 7XSM|1|N, 7XSN|1|N, 7YG8|1|N, 7YG9|1|N, 7YGA|1|N, 7YGB|1|N, 7YGC|1|N, 7YGD|1|N, 8HD6|1|N, 8HD7|1|N, 8I7N|1|N | (0) | (4) 7YC8|1|N, 7YCG|1|N, 7YCH|1|N, 7YCI|1|N |
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.
| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 7XSL|1|N | Misfolded Tetrahymena ribozyme conformation 2 | ELECTRON MICROSCOPY | 3.84 | 388 |
| 2 | 7XSM|1|N | Misfolded Tetrahymena ribozyme conformation 3 | ELECTRON MICROSCOPY | 4.01 | 388 |
| 3 | 7XSK|1|N | Misfolded Tetrahymena ribozyme conformation 1 | ELECTRON MICROSCOPY | 3.53 | 388 |
| 4 | 7UVT|1|A | Kinetically trapped misfolded state of the Tetrahymena ribozyme | ELECTRON MICROSCOPY | 3.9 | 386 |
| 5 | 6WLS|11|A | Tetrahymena ribozyme models, 6.8 Angstrom resolution | ELECTRON MICROSCOPY | 6.8 | 388 |
| 6 | 8HD6|1|N | The relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ELECTRON MICROSCOPY | 3.73 | 419 |
| 7 | 7XD3|1|N | The relaxed pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | ELECTRON MICROSCOPY | 4.05 | 423 |
| 8 | 7EZ0|1|N | Apo L-21 ScaI Tetrahymena ribozyme | ELECTRON MICROSCOPY | 3.14 | 387 |
| 9 | 7XSN|1|N | Native Tetrahymena ribozyme conformation | ELECTRON MICROSCOPY | 3.01 | 387 |
| 10 | 7YGD|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 3.41 | 384 |
| 11 | 7YGC|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 2.65 | 393 |
| 12 | 7YG8|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 5 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 2.97 | 387 |
| 13 | 7XD7|1|N | The pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ELECTRON MICROSCOPY | 3.02 | 405 |
| 14 | 7R6N|1|A | Exon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ELECTRON MICROSCOPY | 4.1 | 354 |
| 15 | 7XD4|1|N | The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon | ELECTRON MICROSCOPY | 3.89 | 423 |
| 16 | 8HD7|1|N | The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ELECTRON MICROSCOPY | 3.52 | 419 |
| 17 | 7XD5|1|N | The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ELECTRON MICROSCOPY | 2.84 | 400 |
| 18 | 8I7N|1|N | The Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ELECTRON MICROSCOPY | 2.98 | 418 |
| 19 | 7EZ2|1|N | Holo L-16 ScaI Tetrahymena ribozyme | ELECTRON MICROSCOPY | 3.05 | 392 |
| 20 | 7XD6|1|N | The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ELECTRON MICROSCOPY | 2.84 | 434 |
| 21 | 7YG9|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 1 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 2.68 | 391 |
| 22 | 7YGA|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 2.35 | 393 |
| 23 | 7YGB|1|N | Cryo-EM structure of Tetrahymena ribozyme conformation 3 undergoing the second-step self-splicing | ELECTRON MICROSCOPY | 2.62 | 393 |
| 24 | 7R6M|1|A | Post-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ELECTRON MICROSCOPY | 3.68 | 356 |
| 25 | 7R6L|1|A | 5 prime exon-free pre-2S intermediate of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic dimeric construct | ELECTRON MICROSCOPY | 2.85 | 343 |
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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