Equivalence class NR_4.0_83593.2 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 | 3WC2|1|P | Transfer RNA | 76mer-tRNA | RF00005 | Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG) | X-ray diffraction | 3.64 | 2013-12-18 | ||
| 7 | 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 |
| 8 | 3WC2|1|Q | Transfer RNA | 76mer-tRNA | RF00005 | Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG) | X-ray diffraction | 3.64 | 2013-12-18 | ||
| 9 | 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 |
| 10 | 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 |
| 11 | 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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 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 |
| 15 | 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 |
| 16 | 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 |
| 17 | 6GZ3|1|Bw | Transfer RNA | pe/E-site-tRNA, mRNA | Saccharomyces cerevisiae | Eukarya | RF00005 | 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 |
| 18 | 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 |
| 19 | 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 |
| 20 | 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 | ||
| 21 | 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 |
| 22 | 6GQV|1|AY | Transfer RNA | Transfer RNA - Phe, Messenger RNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) | Electron microscopy | 4 | 2018-07-11 |
| 23 | 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 |
| 24 | 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 |
| 25 | 6GQB|1|AX | Transfer RNA | Transfer RNA - Phe, Messenger RNA | Saccharomyces cerevisiae | Eukarya | RF00005 | Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin) | Electron microscopy | 3.9 | 2018-07-11 |
| 26 | 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 | ||
| 27 | 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 | ||
| 28 | 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 | 3.152 | 3.153 | 3.154 | 3.155 | 3.156 | 3.157 | 3.158 | 3.159 | 3.160 | 3.161 | 3.162 | 3.163 | 3.164 | 3.165 | 3.166 | 3.167 | 3.168 | 3.169 | 3.170 | 3.171 | 3.172 | 3.173 | 3.174 | 3.175 | 3.176 | 3.177 | 3.178 | 3.179 | 3.180 | 3.181 | 3.182 | 3.183 | 3.184 | 3.185 | 3.186 | 3.187 | 3.188 | 3.189 | 3.190 | 3.191 | 3.192 | 3.193 | 3.194 | 3.195 | 3.196 | 3.197 | 3.198 | 3.199 | 3.200 | 3.201 | 3.202 | 3.203 | 3.204 | 3.205 | 3.206 | 3.207 | 3.208 | 3.209 | 3.210 | 3.211 | 3.212 | 3.213 | 3.214 | 3.215 | 3.216 | 3.217 | 3.218 | 3.219 | 3.220 | 3.221 | 3.222 | 3.223 | 3.224 | 3.225 | 3.226 | 3.227 | 3.228 | 3.229 | 3.230 | 3.231 | 3.232 | 3.233 | 3.234 | 3.235 | 3.236 | 3.237 | 3.238 | 3.239 | 3.240 | 3.241 | 3.242 | 3.243 | 3.244 | 3.245 | 3.246 | 3.247 | 3.248 | 3.249 | 3.250 | 3.251 | 3.252 | 3.253 | 3.254 | 3.255 | 3.256 | 3.257 | 3.258 | 3.259 |
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| Date | 2020-11-11 | 2020-11-18 | 2020-11-25 | 2020-12-02 | 2020-12-09 | 2020-12-16 | 2020-12-23 | 2020-12-30 | 2021-01-06 | 2021-01-13 | 2021-01-20 | 2021-01-27 | 2021-02-03 | 2021-02-10 | 2021-02-17 | 2021-02-24 | 2021-03-03 | 2021-03-10 | 2021-03-17 | 2021-03-24 | 2021-03-31 | 2021-04-07 | 2021-04-14 | 2021-04-21 | 2021-04-28 | 2021-05-05 | 2021-05-12 | 2021-05-19 | 2021-05-26 | 2021-06-02 | 2021-06-09 | 2021-06-16 | 2021-06-23 | 2021-06-30 | 2021-07-07 | 2021-07-14 | 2021-07-21 | 2021-07-28 | 2021-08-04 | 2021-08-11 | 2021-08-18 | 2021-08-25 | 2021-09-01 | 2021-09-08 | 2021-09-15 | 2021-09-22 | 2021-09-29 | 2021-10-06 | 2021-10-13 | 2021-10-20 | 2021-10-27 | 2021-11-03 | 2021-11-10 | 2021-11-17 | 2021-11-24 | 2021-12-01 | 2021-12-08 | 2021-12-15 | 2021-12-22 | 2021-12-29 | 2022-01-05 | 2022-01-12 | 2022-01-19 | 2022-01-26 | 2022-02-02 | 2022-02-09 | 2022-02-16 | 2022-02-23 | 2022-03-02 | 2022-03-09 | 2022-03-16 | 2022-03-23 | 2022-03-30 | 2022-04-06 | 2022-04-13 | 2022-04-20 | 2022-04-27 | 2022-05-04 | 2022-05-11 | 2022-05-18 | 2022-05-25 | 2022-06-01 | 2022-06-08 | 2022-06-15 | 2022-06-22 | 2022-06-29 | 2022-07-06 | 2022-07-13 | 2022-07-20 | 2022-07-27 | 2022-08-03 | 2022-08-10 | 2022-08-17 | 2022-08-24 | 2022-08-31 | 2022-09-07 | 2022-09-14 | 2022-09-21 | 2022-09-28 | 2022-10-05 | 2022-10-12 | 2022-10-19 | 2022-10-26 | 2022-11-02 | 2022-11-09 | 2022-11-16 | 2022-11-23 | 2022-11-30 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_83593.2 | NR_4.0_83593.1 | 3.152 | (28) 1EHZ|1|A, 5AXN|1|P, 5M1J|1|A3, 6GQB|1|AX, 6GQV|1|AY, 6GZ3|1|Bw, 6GZ5|1|Bw, 6LVR|1|B, 6LVR|1|D, 6TNA|1|A, 6XIR|1|AX, 6XIR|1|AZ, 6XZ7|1|g, 5AXM|1|P, 4TRA|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, 3WC2|1|P, 3WC2|1|Q, 4TNA|1|A, 6XZB|1|g2 | (0) | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_4.0_83593.2 | NR_4.0_83593.3 | 3.260 | (28) 1EVV|1|A, 6GQB|1|AX, 1EHZ|1|A, 5M1J|1|A3, 5AXN|1|P, 5AXM|1|P, 4TRA|1|A, 4TNA|1|A, 3WC2|1|Q, 6XZB|1|g2, 3WC2|1|P, 6XZ7|1|g, 1TTT|1|F, 6XIR|1|AZ, 1TTT|1|E, 6XIR|1|AX, 1TTT|1|D, 6TNA|1|A, 1TRA|1|A, 6LVR|1|D, 1TN2|1|A, 6LVR|1|B, 1TN1|1|A, 6GZ5|1|Bw, 1OB2|1|B, 6GZ3|1|Bw, 1I9V|1|A, 6GQV|1|AY | (0) | (1) 8CTH|1|C |
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 | 3WC2|1|P | Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG) | X-RAY DIFFRACTION | 3.64 | 74 |
| 2 | 3WC2|1|Q | Crystal structure of C. albicans tRNA(His) guanylyltransferase (Thg1) with a tRNA(Phe)(GUG) | X-RAY DIFFRACTION | 3.64 | 73 |
| 3 | 5M1J|1|A3 | Nonstop ribosomal complex bound with Dom34 and Hbs1 | ELECTRON MICROSCOPY | 3.3 | 62 |
| 4 | 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 |
| 5 | 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 |
| 6 | 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 |
| 7 | 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 |
| 8 | 5AXM|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) | X-RAY DIFFRACTION | 2.21 | 72 |
| 9 | 5AXN|1|P | Crystal structure of Thg1 like protein (TLP) with tRNA(Phe) and GDPNP | X-RAY DIFFRACTION | 2.7 | 65 |
| 10 | 1TN1|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE TRNA | X-RAY DIFFRACTION | 3 | 62 |
| 11 | 1TN2|1|A | CRYSTALLOGRAPHIC AND BIOCHEMICAL INVESTIGATION OF THE LEAD(II)-CATALYZED HYDROLYSIS OF YEAST PHENYLALANINE T-RNA | 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 | 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 |
| 14 | 1EHZ|1|A | The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution | X-RAY DIFFRACTION | 1.93 | 62 |
| 15 | 6TNA|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE T-RNA. I.CRYSTALLOGRAPHIC REFINEMENT | X-RAY DIFFRACTION | 2.7 | 62 |
| 16 | 4TRA|1|A | RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS | X-RAY DIFFRACTION | 3 | 62 |
| 17 | 1EVV|1|A | CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRANSFER RNA AT 2.0 A RESOLUTION | X-RAY DIFFRACTION | 2 | 62 |
| 18 | 1I9V|1|A | CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX | X-RAY DIFFRACTION | 2.6 | 74 |
| 19 | 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 |
| 20 | 1TTT|1|E | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 21 | 1TTT|1|F | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 22 | 1TTT|1|D | Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex | X-RAY DIFFRACTION | 2.7 | 62 |
| 23 | 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 |
| 24 | 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 |
| 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 | 6GQV|1|AY | Cryo-EM recosntruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GMPPCP) | ELECTRON MICROSCOPY | 4 | 76 |
| 27 | 6XIR|1|AZ | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |
| 28 | 6XIR|1|AX | Cryo-EM Structure of K63 Ubiquitinated Yeast Translocating Ribosome under Oxidative Stress | ELECTRON MICROSCOPY | 3.2 | 73 |