Equivalence class NR_3.5_30153.8 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 | 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 |
| 3 | 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 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 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 |
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 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 |
| 18 | 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
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_3.5_30153.8 | NR_3.5_30153.7 | 3.141 | (16) 6XZ7|1|g, 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, 1TRA|1|A, 1TN2|1|A, 1TN1|1|A, 1OB2|1|B, 1I9V|1|A, 1EHZ|1|A | (2) 6XIR|1|AX, 6XIR|1|AZ | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_3.5_30153.8 | NR_3.5_83593.1 | 3.151 | (18) 1TRA|1|A, 5AXM|1|P, 6GZ5|1|Bw, 6TNA|1|A, 6XZ7|1|g, 1I9V|1|A, 1TN2|1|A, 4TRA|1|A, 5M1J|1|A3, 6LVR|1|D, 6XIR|1|AZ, 1EHZ|1|A, 1TN1|1|A, 4TNA|1|A, 5AXN|1|P, 6LVR|1|B, 6XIR|1|AX, 1OB2|1|B | (0) | (5) 1EVV|1|A, 1TTT|1|D, 1TTT|1|E, 1TTT|1|F, 6XZB|1|g2 |
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 | 1I9V|1|A | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 74 |
| 2 | 4TRA|1|A | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 62 |
| 3 | 6TNA|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 62 |
| 4 | 1EHZ|1|A | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 62 |
| 5 | 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 |
| 6 | 4TNA|1|A | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-RAY DIFFRACTION | 2.5 | 62 |
| 7 | 1TN1|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 62 |
| 8 | 1TN2|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-RAY DIFFRACTION | 3 | 62 |
| 9 | 5AXN|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-RAY DIFFRACTION | 2.7 | 65 |
| 10 | 5AXM|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 72 |
| 11 | 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 |
| 12 | 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 |
| 13 | 5M1J|1|A3 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 62 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 6XIR|1|AZ | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |
| 18 | 6XIR|1|AX | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |