Equivalence class NR_4.0_76703.9 Current
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5E81|1|1K (rep) | Transfer RNA | mRNA, tRNA-Lys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair | X-ray diffraction | 2.95 | 2016-01-27 |
| 2 | 5EL6|1|1L | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin | X-ray diffraction | 3.1 | 2016-01-27 |
| 3 | 5EL4|1|1K | Transfer RNA | mRNA, tRNA-Lys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position | X-ray diffraction | 3.15 | 2016-01-27 |
| 4 | 5IB8|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site | X-ray diffraction | 3.13 | 2016-05-25 |
| 5 | 5IB7|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin | X-ray diffraction | 2.99 | 2016-05-25 |
| 6 | 5E7K|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site | X-ray diffraction | 3.2 | 2016-01-27 |
| 7 | 5EL4|1|1L | Transfer RNA | mRNA, tRNA-Lys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position | X-ray diffraction | 3.15 | 2016-01-27 |
| 8 | 5EL6|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin | X-ray diffraction | 3.1 | 2016-01-27 |
| 9 | 5EL7|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin | X-ray diffraction | 3.15 | 2016-01-27 |
| 10 | 5E81|1|1L | Transfer RNA | mRNA, tRNA-Lys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair | X-ray diffraction | 2.95 | 2016-01-27 |
| 11 | 5IB7|1|1L | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin | X-ray diffraction | 2.99 | 2016-05-25 |
| 12 | 5E7K|1|1L | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site | X-ray diffraction | 3.2 | 2016-01-27 |
| 13 | 5EL7|1|1L | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin | X-ray diffraction | 3.15 | 2016-01-27 |
| 14 | 5EL5|1|1K | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position | X-ray diffraction | 3.15 | 2016-01-27 |
| 15 | 5EL5|1|1L | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position | X-ray diffraction | 3.15 | 2016-01-27 |
| 16 | 8BF7|1|5 | Transfer RNA | Dipeptidyl A-site tRNA(Lys), mRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | Electron microscopy | 2.33 | 2023-08-16 |
| 17 | 7N1P|1|Pt | Transfer RNA | mRNA, tRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | Electron microscopy | 2.33 | 2021-07-14 |
| 18 | 7N2U|1|Pt | Transfer RNA | mRNA, tRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformation | Electron microscopy | 2.53 | 2021-07-14 |
| 19 | 8BH4|1|5 | Transfer RNA | Dipeptidyl A-site tRNA(Lys), mRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | Electron microscopy | 2.62 | 2023-08-16 |
| 20 | 7N30|1|Pt | Transfer RNA | mRNA, tRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformation | Electron microscopy | 2.66 | 2021-07-14 |
| 21 | 7N31|1|Pt | Transfer RNA | mRNA, tRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating 70S ribosome complex in a post-translocation (POST) conformation | Electron microscopy | 2.69 | 2021-07-14 |
| 22 | 7N2C|1|Pt | Transfer RNA | Chains: mR, Chains: Pt | Escherichia coli | Bacteria | RF00005 | Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2) | Electron microscopy | 2.72 | 2021-07-14 |
| 23 | 8BHJ|1|5 | Transfer RNA | Dipeptidyl A-site tRNA(Lys), mRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | Electron microscopy | 2.81 | 2023-08-16 |
| 24 | 7ZTA|1|PTR1 | Transfer RNA | mRNA, tRNA-Lys | Escherichia coli K-12 | Bacteria | RF00005 | Structure of an Escherichia coli 70S ribosome stalled by Tetracenomycin X during translation of an MAAAPQK(C) peptide | Electron microscopy | 2.7 | 2023-04-12 |
| 25 | 8BHN|1|5 | Transfer RNA | Dipeptidyl A-site tRNA(Lys), mRNA | Escherichia coli K-12 | Bacteria | RF00005 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | Electron microscopy | 2.85 | 2023-08-16 |
| 26 | 7D6Z|1|4 | Transfer RNA | A-site tRNA | Escherichia coli | Bacteria | RF00005 | Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor | Electron microscopy | 3.4 | 2021-04-07 |
| 27 | 8FON|1|QV | Transfer RNA | mRNA, P-site tRNA^Lys(SUU) | Escherichia coli | Bacteria | RF00005 | Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P site | X-ray diffraction | 3.64 | 2023-03-29 |
| 28 | 8FON|1|XV | Transfer RNA | A-site ASL^Phe, mRNA, P-site tRNA^Lys(SUU) | Escherichia coli | Bacteria | RF00005 | Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P site | X-ray diffraction | 3.64 | 2023-03-29 |
| 29 | 5UYQ|1|Y | Transfer RNA | mRNA, tRNALys | Escherichia coli | Bacteria | RF00005 | 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc) | Electron microscopy | 3.8 | 2017-06-07 |
| 30 | 5JTE|1|AW | Transfer RNA | A-site Lysine tRNA Lysine, mRNA | Escherichia coli | Bacteria | RF00005 | Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA | Electron microscopy | 3.6 | 2016-07-20 |
| 31 | 8FOM|1|QV | Transfer RNA | mRNA, P-site tRNA^Lys(SUU) | Escherichia coli | Bacteria | RF00005 | Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site | X-ray diffraction | 3.58 | 2023-03-29 |
| 32 | 8FOM|1|XV | Transfer RNA | mRNA, P-site tRNA^Lys(SUU) | Escherichia coli | Bacteria | RF00005 | Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site | X-ray diffraction | 3.58 | 2023-03-29 |
| 33 | 5UYP|1|Y | Transfer RNA | tRNALys | Escherichia coli | Bacteria | RF00005 | 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc) | Electron microscopy | 3.9 | 2017-06-07 |
| 34 | 5UYN|1|Y | Transfer RNA | tRNALys | Escherichia coli | Bacteria | RF00005 | 70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc) | Electron microscopy | 4 | 2017-06-07 |
Release history
| Release | 3.296 | 3.297 | 3.298 | 3.299 | 3.300 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2023-08-16 | 2023-08-23 | 2023-08-30 | 2023-09-06 | 2023-09-13 | 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 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_4.0_76703.9 | NR_4.0_76703.8 | 3.296 | (30) 5E7K|1|1K, 5E7K|1|1L, 5E81|1|1K, 5E81|1|1L, 5EL4|1|1K, 5EL4|1|1L, 5EL5|1|1K, 5EL5|1|1L, 5EL6|1|1K, 5EL6|1|1L, 5EL7|1|1K, 5EL7|1|1L, 5IB7|1|1K, 5IB7|1|1L, 5IB8|1|1K, 5JTE|1|AW, 5UYN|1|Y, 5UYP|1|Y, 5UYQ|1|Y, 7D6Z|1|4, 7N1P|1|Pt, 7N2C|1|Pt, 7N2U|1|Pt, 7N30|1|Pt, 7N31|1|Pt, 7ZTA|1|PTR1, 8FOM|1|QV, 8FOM|1|XV, 8FON|1|QV, 8FON|1|XV | (4) 8BF7|1|5, 8BH4|1|5, 8BHJ|1|5, 8BHN|1|5 | (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 | PDB | Title | Method | Resolution | Length |
|---|---|---|---|---|---|
| 1 | 5EL5|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position | X-RAY DIFFRACTION | 3.15 | 64 |
| 2 | 8BHJ|1|5 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and Am6AA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | ELECTRON MICROSCOPY | 2.81 | 70 |
| 3 | 8BH4|1|5 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAm6A mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | ELECTRON MICROSCOPY | 2.62 | 70 |
| 4 | 8BF7|1|5 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | ELECTRON MICROSCOPY | 2.33 | 70 |
| 5 | 8BHN|1|5 | Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site | ELECTRON MICROSCOPY | 2.85 | 70 |
| 6 | 7ZTA|1|PTR1 | Structure of an Escherichia coli 70S ribosome stalled by Tetracenomycin X during translation of an MAAAPQK(C) peptide | ELECTRON MICROSCOPY | 2.7 | 66 |
| 7 | 8FON|1|QV | Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P site | X-RAY DIFFRACTION | 3.64 | 72 |
| 8 | 8FON|1|XV | Crystal structure of tRNA^Lys(SUU) bound to AUA codon in the ribosomal P site | X-RAY DIFFRACTION | 3.64 | 72 |
| 9 | 8FOM|1|XV | Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site | X-RAY DIFFRACTION | 3.58 | 66 |
| 10 | 8FOM|1|QV | Crystal structure of tRNA^Lys(SUU) bound to UAA codon in the ribosomal P site | X-RAY DIFFRACTION | 3.58 | 66 |
| 11 | 7N31|1|Pt | Elongating 70S ribosome complex in a post-translocation (POST) conformation | ELECTRON MICROSCOPY | 2.69 | 67 |
| 12 | 7N2C|1|Pt | Elongating 70S ribosome complex in a fusidic acid-stalled intermediate state of translocation bound to EF-G(GDP) (INT2) | ELECTRON MICROSCOPY | 2.72 | 67 |
| 13 | 7N2U|1|Pt | Elongating 70S ribosome complex in a hybrid-H1 pre-translocation (PRE-H1) conformation | ELECTRON MICROSCOPY | 2.53 | 67 |
| 14 | 7N30|1|Pt | Elongating 70S ribosome complex in a hybrid-H2* pre-translocation (PRE-H2*) conformation | ELECTRON MICROSCOPY | 2.66 | 66 |
| 15 | 7N1P|1|Pt | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ELECTRON MICROSCOPY | 2.33 | 67 |
| 16 | 7D6Z|1|4 | Molecular model of the cryo-EM structure of 70S ribosome in complex with peptide deformylase and trigger factor | ELECTRON MICROSCOPY | 3.4 | 66 |
| 17 | 5JTE|1|AW | Cryo-EM structure of an ErmBL-stalled ribosome in complex with A-, P-, and E-tRNA | ELECTRON MICROSCOPY | 3.6 | 66 |
| 18 | 5E81|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair | X-RAY DIFFRACTION | 2.95 | 67 |
| 19 | 5IB7|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin | X-RAY DIFFRACTION | 2.99 | 67 |
| 20 | 5IB8|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site | X-RAY DIFFRACTION | 3.13 | 66 |
| 21 | 5E7K|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site | X-RAY DIFFRACTION | 3.2 | 66 |
| 22 | 5EL4|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position | X-RAY DIFFRACTION | 3.15 | 64 |
| 23 | 5EL6|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin | X-RAY DIFFRACTION | 3.1 | 64 |
| 24 | 5EL7|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin | X-RAY DIFFRACTION | 3.15 | 64 |
| 25 | 5EL5|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position | X-RAY DIFFRACTION | 3.15 | 71 |
| 26 | 5EL7|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin | X-RAY DIFFRACTION | 3.15 | 68 |
| 27 | 5EL4|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position | X-RAY DIFFRACTION | 3.15 | 72 |
| 28 | 5EL6|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin | X-RAY DIFFRACTION | 3.1 | 68 |
| 29 | 5E7K|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site | X-RAY DIFFRACTION | 3.2 | 68 |
| 30 | 5E81|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with wobble pair | X-RAY DIFFRACTION | 2.95 | 64 |
| 31 | 5IB7|1|1L | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin | X-RAY DIFFRACTION | 2.99 | 66 |
| 32 | 5UYN|1|Y | 70S ribosome bound with near-cognate ternary complex not base-paired to A site codon (Structure I-nc) | ELECTRON MICROSCOPY | 4 | 75 |
| 33 | 5UYP|1|Y | 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, open 30S (Structure II-nc) | ELECTRON MICROSCOPY | 3.9 | 75 |
| 34 | 5UYQ|1|Y | 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc) | ELECTRON MICROSCOPY | 3.8 | 75 |
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.
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