Equivalence class NR_all_30153.8 Obsolete
| # | IFE | Compound(s) | RNA source organism | Title | Method | Resolution | Date |
|---|---|---|---|---|---|---|---|
| 1 | 5AXM|1|P (rep) | RNA (75-MER) | Saccharomyces cerevisiae | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 2016-08-03 |
| 2 | 5AXN|1|P | RNA (75-MER) | Saccharomyces cerevisiae | 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, PHE | Saccharomyces cerevisiae | 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 | yeast phenylalanine tRNA | Saccharomyces cerevisiae | 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 | yeast phenylalanine tRNA | Saccharomyces cerevisiae | 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 | TRNAPHE | Saccharomyces cerevisiae | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-RAY DIFFRACTION | 2.5 | 1978-04-12 |
| 7 | 1EHZ|1|A | TRANSFER RNA (PHE) | Saccharomyces cerevisiae | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 2000-10-02 |
| 8 | 6XZ7|1|g | fMet-Phe-tRNA(Phe) | Saccharomyces cerevisiae | 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 | PHENYLALANINE TRANSFER RNA | Saccharomyces cerevisiae | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 2001-06-04 |
| 10 | 6XIR|1|AZ | Transfer RNA | Saccharomyces cerevisiae | 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 | Saccharomyces cerevisiae | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 2020-08-26 |
| 12 | 6GZ5|1|Bw | E/E-site-tRNA, mRNA | Saccharomyces cerevisiae | 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 | 6GZ3|1|Bw | pe/E-site-tRNA, mRNA | Saccharomyces cerevisiae | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1) | ELECTRON MICROSCOPY | 3.6 | 2018-12-05 |
| 14 | 1TN1|1|A | TRNAPHE | Saccharomyces cerevisiae | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 1987-01-15 |
| 15 | 1TN2|1|A | TRNAPHE | Saccharomyces cerevisiae | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-RAY DIFFRACTION | 3 | 1986-10-24 |
| 16 | 5M1J|1|A3 | yeast Phe-tRNA-Phe, nonstop mRNA | Saccharomyces cerevisiae | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 2017-01-18 |
| 17 | 6GQV|1|AY | Transfer RNA - Phe, Messenger RNA | Saccharomyces cerevisiae | Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) | ELECTRON MICROSCOPY | 4 | 2018-07-11 |
| 18 | 4TRA|1|A | TRNAPHE | Saccharomyces cerevisiae | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 1987-11-06 |
| 19 | 6TNA|1|A | TRNAPHE | Saccharomyces cerevisiae | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 1979-01-16 |
| 20 | 6GQB|1|AX | Transfer RNA - Phe, Messenger RNA | Saccharomyces cerevisiae | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) | ELECTRON MICROSCOPY | 3.9 | 2018-07-11 |
| 21 | 6XIQ|1|AX | Transfer RNA | Saccharomyces cerevisiae | Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 4.2 | 2020-08-26 |
| 22 | 6XIQ|1|AZ | Transfer RNA | Saccharomyces cerevisiae | Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 4.2 | 2020-08-26 |
| 23 | 6GQ1|1|AX | Transfer RNA - Phe, Messenger RNA | Saccharomyces cerevisiae | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) | ELECTRON MICROSCOPY | 4.4 | 2018-07-11 |
| 24 | 1TRA|1|A | TRNAPHE | Saccharomyces cerevisiae | 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 |
| 25 | 1LS2|1|B | Phenylalanine transfer RNA | Saccharomyces cerevisiae | Fitting of EF-Tu and tRNA in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome | ELECTRON MICROSCOPY | 16.8 | 2002-06-26 |
| 26 | 1FCW|1|A | TRNAPHE | Saccharomyces cerevisiae | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 2000-08-11 |
| 27 | 1FCW|1|D | TRNAPHE | Saccharomyces cerevisiae | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 2000-08-11 |
| 28 | 1FCW|1|B | TRNAPHE | Saccharomyces cerevisiae | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 2000-08-11 |
| 29 | 1FCW|1|E | TRNAPHE | Saccharomyces cerevisiae | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 2000-08-11 |
| 30 | 1FCW|1|C | TRNAPHE | Saccharomyces cerevisiae | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 2000-08-11 |
Release history
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_30153.8 | NR_all_30153.7 | 3.141 | (26) 4TRA|1|A, 6GZ5|1|Bw, 1FCW|1|E, 4TNA|1|A, 6GZ3|1|Bw, 1FCW|1|D, 1TRA|1|A, 6GQV|1|AY, 1FCW|1|C, 1TN2|1|A, 6GQB|1|AX, 1FCW|1|B, 1TN1|1|A, 6GQ1|1|AX, 1FCW|1|A, 6XZ7|1|g, 1OB2|1|B, 5M1J|1|A3, 1EHZ|1|A, 6TNA|1|A, 1LS2|1|B, 5AXN|1|P, 6LVR|1|D, 1I9V|1|A, 5AXM|1|P, 6LVR|1|B | (4) 6XIQ|1|AX, 6XIR|1|AZ, 6XIR|1|AX, 6XIQ|1|AZ | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_30153.8 | NR_all_83593.1 | 3.151 | (30) 6GQB|1|AX, 6XIR|1|AZ, 1FCW|1|C, 4TRA|1|A, 6LVR|1|D, 1TN1|1|A, 6GQV|1|AY, 1FCW|1|D, 5AXM|1|P, 6TNA|1|A, 1EHZ|1|A, 1TN2|1|A, 6GZ3|1|Bw, 1FCW|1|E, 6XZ7|1|g, 5AXN|1|P, 6XIQ|1|AX, 1FCW|1|A, 1TRA|1|A, 1I9V|1|A, 5M1J|1|A3, 6XIQ|1|AZ, 1FCW|1|B, 6GZ5|1|Bw, 1LS2|1|B, 6GQ1|1|AX, 6XIR|1|AX, 4TNA|1|A, 6LVR|1|B, 1OB2|1|B | (0) | (18) 1JGP|1|B, 1EVV|1|A, 4V69|1|AY, 3WC2|1|Q, 1TTT|1|E, 1JGP|1|C, 1JGO|1|C, 4V42|1|AB, 6XZB|1|g2, 1TTT|1|F, 1SZ1|1|F, 1JGQ|1|C, 3WC2|1|P, 4V42|1|AC, 1TTT|1|D, 1JGO|1|B, 1SZ1|1|E, 1JGQ|1|B |
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 | 1LS2|1|B | Fitting of EF-Tu and tRNA in the Low Resolution Cryo-EM Map of an EF-Tu Ternary Complex (GDP and Kirromycin) Bound to E. coli 70S Ribosome | ELECTRON MICROSCOPY | 16.8 | 76 |
| 2 | 1I9V|1|A | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 74 |
| 3 | 1FCW|1|C | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 62 |
| 4 | 1FCW|1|A | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 62 |
| 5 | 1FCW|1|B | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 62 |
| 6 | 1FCW|1|D | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 62 |
| 7 | 1FCW|1|E | TRNA POSITIONS DURING THE ELONGATION CYCLE | ELECTRON MICROSCOPY | 17 | 62 |
| 8 | 4TRA|1|A | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 62 |
| 9 | 6TNA|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 62 |
| 10 | 1EHZ|1|A | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 62 |
| 11 | 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 |
| 12 | 4TNA|1|A | FURTHER REFINEMENT OF THE STRUCTURE OF YEAST T-RNA-PHE | X-RAY DIFFRACTION | 2.5 | 62 |
| 13 | 1TN1|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 62 |
| 14 | 1TN2|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | X-RAY DIFFRACTION | 3 | 62 |
| 15 | 5AXN|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-RAY DIFFRACTION | 2.7 | 65 |
| 16 | 5AXM|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 72 |
| 17 | 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 |
| 18 | 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 |
| 19 | 5M1J|1|A3 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 62 |
| 20 | 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 |
| 21 | 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 |
| 22 | 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 |
| 23 | 6GZ3|1|Bw | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1) | ELECTRON MICROSCOPY | 3.6 | 76 |
| 24 | 6GQV|1|AY | Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) | ELECTRON MICROSCOPY | 4 | 76 |
| 25 | 6GQB|1|AX | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) | ELECTRON MICROSCOPY | 3.9 | 76 |
| 26 | 6GQ1|1|AX | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP/sordarin) | ELECTRON MICROSCOPY | 4.4 | 76 |
| 27 | 6XIR|1|AX | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |
| 28 | 6XIR|1|AZ | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |
| 29 | 6XIQ|1|AZ | Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 4.2 | 76 |
| 30 | 6XIQ|1|AX | Cryo-EM Structure of K63R Ubiquitin Mutant Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 4.2 | 76 |