Equivalence class NR_3.5_83593.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 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 | 2000-10-02 |
| 9 | 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 | 2020-07-22 |
| 10 | 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 | 2001-06-04 |
| 11 | 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 | 2020-11-04 |
| 12 | 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 | 2020-08-26 |
| 13 | 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 | 2020-08-26 |
| 14 | 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 | 2018-12-05 |
| 15 | 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 | 1987-01-15 |
| 16 | 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 | 1986-10-24 |
| 17 | 1TTT|1|F | Transfer RNA | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | RF00005 | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 1996-12-23 | ||
| 18 | 5M1J|1|A3 | Transfer RNA | yeast Phe-tRNA-Phe, nonstop mRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | Electron microscopy | 3.3 | 2017-01-18 |
| 19 | 8CTH|1|C | Phe-tRNA | Saccharomyces cerevisiae | Eukarya | Cryo-EM structure of human METTL1-WDR4-tRNA(Phe) complex | Electron microscopy | 3.3 | 2022-12-07 | ||
| 20 | 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 | 1987-11-06 |
| 21 | 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 | 1979-01-16 |
| 22 | 1TTT|1|D | Transfer RNA | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | RF00005 | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 1996-12-23 | ||
| 23 | 1TTT|1|E | Transfer RNA | TRANSFER RIBONUCLEIC ACID (YEAST, PHE) | RF00005 | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-ray diffraction | 2.7 | 1996-12-23 | ||
| 24 | 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 | 1986-07-14 |
Release history
| Release | 3.260 | 3.261 | 3.262 | 3.263 | 3.264 | 3.265 | 3.266 | 3.267 | 3.268 | 3.269 | 3.270 | 3.271 | 3.272 | 3.273 | 3.274 | 3.275 | 3.276 | 3.277 | 3.278 | 3.279 | 3.280 | 3.281 | 3.282 | 3.283 | 3.284 | 3.285 | 3.286 | 3.287 | 3.288 | 3.289 | 3.290 | 3.291 | 3.292 | 3.293 | 3.294 | 3.295 | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2022-12-07 | 2022-12-14 | 2022-12-21 | 2022-12-28 | 2023-01-04 | 2023-01-11 | 2023-01-18 | 2023-01-25 | 2023-02-01 | 2023-02-08 | 2023-02-15 | 2023-02-22 | 2023-03-01 | 2023-03-08 | 2023-03-15 | 2023-03-22 | 2023-03-29 | 2023-04-05 | 2023-04-12 | 2023-04-19 | 2023-04-26 | 2023-05-03 | 2023-05-10 | 2023-05-17 | 2023-05-24 | 2023-05-31 | 2023-06-07 | 2023-06-14 | 2023-06-21 | 2023-06-28 | 2023-07-05 | 2023-07-12 | 2023-07-19 | 2023-07-26 | 2023-08-02 | 2023-08-09 | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_83593.3 | NR_3.5_83593.2 | 3.260 | (23) 1TTT|1|E, 1TTT|1|D, 1TRA|1|A, 1TN2|1|A, 1TN1|1|A, 1OB2|1|B, 1I9V|1|A, 1EVV|1|A, 1EHZ|1|A, 6XZB|1|g2, 6XZ7|1|g, 6XIR|1|AZ, 6XIR|1|AX, 6TNA|1|A, 6LVR|1|D, 6LVR|1|B, 6GZ5|1|Bw, 5M1J|1|A3, 5AXN|1|P, 5AXM|1|P, 4TRA|1|A, 4TNA|1|A, 1TTT|1|F | (1) 8CTH|1|C | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_83593.3 | NR_3.5_83593.4 | 3.301 | (24) 5AXM|1|P, 1I9V|1|A, 5M1J|1|A3, 1TN1|1|A, 6LVR|1|B, 1TRA|1|A, 6TNA|1|A, 1TTT|1|E, 6XIR|1|AZ, 4TNA|1|A, 1EHZ|1|A, 6XZB|1|g2, 1EVV|1|A, 5AXN|1|P, 1OB2|1|B, 6GZ5|1|Bw, 1TN2|1|A, 6LVR|1|D, 1TTT|1|D, 6XIR|1|AX, 1TTT|1|F, 4TRA|1|A, 8CTH|1|C, 6XZ7|1|g | (0) | (8) 8CG8|1|Bb, 8CIV|1|Bb, 8CF5|1|Bb, 8CEH|1|Bb, 8CDR|1|Bb, 8CDL|1|Bb, 8CCS|1|Bb, 8CKU|1|Bb |
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).| #S | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 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 | 62 |
| 5 | 1EHZ|1|A | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 62 |
| 6 | 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 | 62 |
| 7 | 4TNA|1|A | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-RAY DIFFRACTION | 2.5 | 62 |
| 8 | 1TN1|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 62 |
| 9 | 1TN2|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-RAY DIFFRACTION | 3 | 62 |
| 10 | 6TNA|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 62 |
| 11 | 4TRA|1|A | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 62 |
| 12 | 1I9V|1|A | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 74 |
| 13 | 1EVV|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION | X-RAY DIFFRACTION | 2 | 62 |
| 14 | 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 | 58 |
| 15 | 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 | 58 |
| 16 | 5AXM|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 72 |
| 17 | 5AXN|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-RAY DIFFRACTION | 2.7 | 65 |
| 18 | 5M1J|1|A3 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 62 |
| 19 | 6XZ7|1|g | E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet). | ELECTRON MICROSCOPY | 2.1 | 61 |
| 20 | 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 | 61 |
| 21 | 1TTT|1|D | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 22 | 1TTT|1|F | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 23 | 1TTT|1|E | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 24 | 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 | 63 |