Equivalence class NR_3.5_83593.4 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5AXM|1|P (rep) | Transfer RNA | RNA (75-MER) | Saccharomyces cerevisiae | Eukarya | RF00005 | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-ray diffraction | 2.21 | 73 | 2016-08-03 |
| 2 | 1EVV|1|A | Transfer RNA | PHENYLALANINE TRANSFER RNA | Saccharomyces | Eukarya | RF00005 | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION | X-ray diffraction | 2 | 76 | 2000-05-01 |
| 3 | 5AXN|1|P | Transfer RNA | RNA (75-MER) | Saccharomyces cerevisiae | Eukarya | RF00005 | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-ray diffraction | 2.7 | 66 | 2016-08-03 |
| 4 | 1OB2|1|B | Transfer RNA | TRANSFER-RNA, PHE | Saccharomyces cerevisiae | Eukarya | RF00005 | E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA | X-ray diffraction | 3.35 | 76 | 2004-05-27 |
| 5 | 6LVR|1|D | Transfer RNA | yeast phenylalanine tRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA | X-ray diffraction | 2.85 | 72 | 2020-08-12 |
| 6 | 6LVR|1|B | Transfer RNA | yeast phenylalanine tRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA | X-ray diffraction | 2.85 | 72 | 2020-08-12 |
| 7 | 4TNA|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-ray diffraction | 2.5 | 76 | 1978-04-12 |
| 8 | 1EHZ|1|A | Transfer RNA | TRANSFER RNA (PHE) | Saccharomyces cerevisiae | Eukarya | RF00005 | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-ray diffraction | 1.93 | 76 | 2000-10-02 |
| 9 | 8CCS|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex | Electron microscopy | 1.97 | 76 | 2023-09-20 |
| 10 | 8CDR|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | Electron microscopy | 2.04 | 76 | 2023-09-20 |
| 11 | 8CEH|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | Electron microscopy | 2.05 | 76 | 2023-09-20 |
| 12 | 8CIV|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | Electron microscopy | 2.47 | 76 | 2023-09-20 |
| 13 | 8CG8|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | Electron microscopy | 2.57 | 76 | 2023-09-20 |
| 14 | 6XZ7|1|g | Transfer RNA | fMet-Phe-tRNA(Phe) | Saccharomyces cerevisiae | Eukarya | RF00005 | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | Electron microscopy | 2.1 | 76 | 2020-07-22 |
| 15 | 8CF5|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | Electron microscopy | 2.71 | 76 | 2023-09-20 |
| 16 | 8CDL|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex | Electron microscopy | 2.72 | 76 | 2023-09-20 |
| 17 | 1I9V|1|A | Transfer RNA | PHENYLALANINE TRANSFER RNA | Saccharomyces cerevisiae | Eukarya | RF00005 | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-ray diffraction | 2.6 | 76 | 2001-06-04 |
| 18 | 6XZB|1|g2 | Transfer RNA | fMet-Phe-tRNA(Phe) | Saccharomyces cerevisiae | Eukarya | RF00005 | E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification). | Electron microscopy | 2.54 | 76 | 2020-11-04 |
| 19 | 8CKU|1|Bb | Transfer RNA | Messenger RNA, Transfer RNA Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin | Electron microscopy | 3.11 | 76 | 2023-09-20 |
| 20 | 6XIR|1|AZ | Transfer RNA | Transfer RNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | Electron microscopy | 3.2 | 73 | 2020-08-26 |
| 21 | 6XIR|1|AX | Transfer RNA | Transfer RNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | Electron microscopy | 3.2 | 73 | 2020-08-26 |
| 22 | 6GZ5|1|Bw | Transfer RNA | E/E-site-tRNA, mRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3) | Electron microscopy | 3.5 | 76 | 2018-12-05 |
| 23 | 1TN1|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-ray diffraction | 3 | 76 | 1987-01-15 |
| 24 | 1TN2|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-ray diffraction | 3 | 76 | 1986-10-24 |
| 25 | 1TTT|1|F | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 76 | 1996-12-23 | ||||
| 26 | 5M1J|1|A3 | Transfer RNA | nonstop mRNA, yeast Phe-tRNA-Phe | Saccharomyces cerevisiae | Eukarya | RF00005 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | Electron microscopy | 3.3 | 76 | 2017-01-18 |
| 27 | 8CTH|1|C | Transfer RNA | Phe-tRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complex | Electron microscopy | 3.3 | 74 | 2022-12-07 |
| 28 | 4TRA|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-ray diffraction | 3 | 76 | 1987-11-06 |
| 29 | 6TNA|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-ray diffraction | 2.7 | 76 | 1979-01-16 |
| 30 | 1TTT|1|D | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 76 | 1996-12-23 | ||||
| 31 | 1TTT|1|E | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 76 | 1996-12-23 | ||||
| 32 | 1TRA|1|A | Transfer RNA | TRNAPHE | Saccharomyces cerevisiae | Eukarya | RF00005 | RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES | X-ray diffraction | 3 | 76 | 1986-07-14 |
Release history
| Release | 3.301 | 3.302 | 3.303 | 3.304 | 3.305 | 3.306 | 3.307 | 3.308 | 3.309 | 3.310 | 3.311 | 3.312 | 3.313 | 3.314 | 3.315 | 3.316 | 3.317 | 3.318 | 3.319 | 3.320 | 3.321 | 3.322 | 3.323 | 3.324 | 3.325 | 3.326 | 3.327 | 3.328 | 3.329 | 3.330 | 3.331 | 3.332 | 3.333 | 3.334 | 3.335 | 3.336 | 3.337 | 3.338 | 3.339 | 3.340 | 3.341 | 3.342 | 3.343 | 3.344 | 3.345 | 3.346 | 3.347 | 3.348 | 3.349 | 3.350 | 3.351 | 3.352 | 3.353 | 3.354 | 3.355 | 3.356 | 3.357 | 3.358 | 3.359 | 3.360 | 3.361 | 3.362 | 3.363 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2023-09-20 | 2023-09-27 | 2023-10-04 | 2023-10-11 | 2023-10-18 | 2023-10-25 | 2023-11-01 | 2023-11-08 | 2023-11-15 | 2023-11-24 | 2023-11-29 | 2023-12-06 | 2023-12-13 | 2023-12-20 | 2023-12-27 | 2024-01-03 | 2024-01-10 | 2024-01-17 | 2024-01-24 | 2024-01-31 | 2024-02-07 | 2024-02-14 | 2024-02-21 | 2024-02-28 | 2024-03-06 | 2024-03-13 | 2024-03-20 | 2024-03-27 | 2024-04-03 | 2024-04-10 | 2024-04-17 | 2024-04-24 | 2024-05-01 | 2024-05-08 | 2024-05-15 | 2024-05-22 | 2024-05-29 | 2024-06-05 | 2024-06-12 | 2024-06-19 | 2024-06-26 | 2024-07-03 | 2024-07-10 | 2024-07-17 | 2024-07-25 | 2024-07-31 | 2024-08-07 | 2024-08-14 | 2024-08-21 | 2024-08-28 | 2024-09-04 | 2024-09-11 | 2024-09-18 | 2024-09-25 | 2024-10-02 | 2024-10-09 | 2024-10-16 | 2024-10-23 | 2024-10-30 | 2024-11-06 | 2024-11-13 | 2024-11-20 | 2024-11-27 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_83593.4 | NR_3.5_83593.3 | 3.301 | (24) 1EHZ|1|A, 1EVV|1|A, 1I9V|1|A, 1OB2|1|B, 1TN1|1|A, 1TN2|1|A, 1TRA|1|A, 1TTT|1|D, 1TTT|1|E, 1TTT|1|F, 4TNA|1|A, 4TRA|1|A, 5AXM|1|P, 5AXN|1|P, 5M1J|1|A3, 6GZ5|1|Bw, 6LVR|1|B, 6LVR|1|D, 6TNA|1|A, 6XIR|1|AX, 6XIR|1|AZ, 6XZ7|1|g, 6XZB|1|g2, 8CTH|1|C | (8) 8CCS|1|Bb, 8CDL|1|Bb, 8CDR|1|Bb, 8CEH|1|Bb, 8CF5|1|Bb, 8CG8|1|Bb, 8CIV|1|Bb, 8CKU|1|Bb | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added 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.
| #S | View | PDB | Title | Method | Resolution | #NTs |
|---|---|---|---|---|---|---|
| 1 | 6XIR|1|AX | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 | |
| 2 | 6XIR|1|AZ | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 | |
| 3 | 6GZ5|1|Bw | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-3 (TI-POST-3) | ELECTRON MICROSCOPY | 3.5 | 76 | |
| 4 | 8CTH|1|C | Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complex | ELECTRON MICROSCOPY | 3.3 | 74 | |
| 5 | 1EHZ|1|A | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 76 | |
| 6 | 6TNA|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 76 | |
| 7 | 4TRA|1|A | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 76 | |
| 8 | 1TRA|1|A | RESTRAINED REFINEMENT OF THE MONOCLINIC FORM OF YEAST PHENYLALANINE TRANSFER RNA. TEMPERATURE FACTORS AND DYNAMICS, COORDINATED WATERS, AND BASE-PAIR PROPELLER TWIST ANGLES | X-RAY DIFFRACTION | 3 | 76 | |
| 9 | 4TNA|1|A | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-RAY DIFFRACTION | 2.5 | 76 | |
| 10 | 1TN1|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 76 | |
| 11 | 1TN2|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-RAY DIFFRACTION | 3 | 76 | |
| 12 | 1I9V|1|A | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 76 | |
| 13 | 1EVV|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION | X-RAY DIFFRACTION | 2 | 76 | |
| 14 | 5AXM|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 73 | |
| 15 | 5AXN|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-RAY DIFFRACTION | 2.7 | 66 | |
| 16 | 1TTT|1|F | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 76 | |
| 17 | 1TTT|1|E | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 76 | |
| 18 | 1OB2|1|B | E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA | X-RAY DIFFRACTION | 3.35 | 76 | |
| 19 | 1TTT|1|D | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 76 | |
| 20 | 6LVR|1|B | Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA | X-RAY DIFFRACTION | 2.85 | 72 | |
| 21 | 6LVR|1|D | Crystal structure of the PPR domain of Arabidopsis thaliana protein-only RNase P 1 (PRORP1) in complex with tRNA | X-RAY DIFFRACTION | 2.85 | 72 | |
| 22 | 6XZB|1|g2 | E. coli 70S ribosome in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet) (focused classification). | ELECTRON MICROSCOPY | 2.54 | 76 | |
| 23 | 6XZ7|1|g | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | ELECTRON MICROSCOPY | 2.1 | 76 | |
| 24 | 5M1J|1|A3 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 76 | |
| 25 | 8CEH|1|Bb | Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | ELECTRON MICROSCOPY | 2.05 | 76 | |
| 26 | 8CDR|1|Bb | Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | ELECTRON MICROSCOPY | 2.04 | 76 | |
| 27 | 8CG8|1|Bb | Translocation intermediate 3 (TI-3) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | ELECTRON MICROSCOPY | 2.57 | 76 | |
| 28 | 8CIV|1|Bb | Translocation intermediate 5 (TI-5) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | ELECTRON MICROSCOPY | 2.47 | 76 | |
| 29 | 8CCS|1|Bb | 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex | ELECTRON MICROSCOPY | 1.97 | 76 | |
| 30 | 8CDL|1|Bb | 80S S. cerevisiae ribosome with ligands in hybrid-2 pre-translocation (PRE-H2) complex | ELECTRON MICROSCOPY | 2.72 | 76 | |
| 31 | 8CF5|1|Bb | Translocation intermediate 1 (TI-1) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin | ELECTRON MICROSCOPY | 2.71 | 76 | |
| 32 | 8CKU|1|Bb | Translocation intermediate 1 (TI-1*) of 80S S. cerevisiae ribosome with ligands and eEF2 in the absence of sordarin | ELECTRON MICROSCOPY | 3.11 | 76 |
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.
Coloring options: