Equivalence class NR_all_69813.3 Obsolete
| # | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | Date |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 5IBB|1|1K (rep) | Transfer RNA | tRNAVal, mRNA | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-ray diffraction | 2.96 | 2016-05-25 |
| 2 | 6CAE|1|1y | Transfer RNA | A-site and E-site tRNAs | Escherichia coli | Bacteria | RF00005 | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-ray diffraction | 2.6 | 2018-04-18 |
| 3 | 5IBB|1|3L | Transfer RNA | tRNAVal | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-ray diffraction | 2.96 | 2016-05-25 |
| 4 | 6CAE|1|1w | Transfer RNA | A-site and E-site tRNAs, mRNA | Escherichia coli | Bacteria | RF00005 | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-ray diffraction | 2.6 | 2018-04-18 |
| 5 | 6CAE|1|2y | Transfer RNA | A-site and E-site tRNAs | Escherichia coli | Bacteria | RF00005 | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-ray diffraction | 2.6 | 2018-04-18 |
| 6 | 6CAE|1|2w | Transfer RNA | A-site and E-site tRNAs, mRNA | Escherichia coli | Bacteria | RF00005 | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-ray diffraction | 2.6 | 2018-04-18 |
| 7 | 5IBB|1|3K | Transfer RNA | tRNAVal | Escherichia coli | Bacteria | RF00005 | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-ray diffraction | 2.96 | 2016-05-25 |
| 8 | 4V7A|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4) | Electron microscopy | 9 | 2014-07-09 |
| 9 | 4V6Y|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a) | Electron microscopy | 12 | 2014-07-09 |
| 10 | 4V75|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1) | Electron microscopy | 12 | 2014-07-09 |
| 11 | 4V6Z|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b) | Electron microscopy | 12 | 2014-07-09 |
| 12 | 4V72|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4) | Electron microscopy | 13 | 2014-07-09 |
| 13 | 4V79|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b) | Electron microscopy | 15 | 2014-07-09 |
| 14 | 4V73|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a) | Electron microscopy | 15 | 2014-07-09 |
| 15 | 4V70|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3) | Electron microscopy | 17 | 2014-07-09 |
| 16 | 4V76|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a) | Electron microscopy | 17 | 2014-07-09 |
| 17 | 4V77|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b) | Electron microscopy | 17 | 2014-07-09 |
| 18 | 4V74|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b) | Electron microscopy | 17 | 2014-07-09 |
| 19 | 4V78|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a) | Electron microscopy | 20 | 2014-07-09 |
| 20 | 4V71|1|A1 | Transfer RNA | fMet-Val-tRNA-Val, 5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3' | Escherichia coli | Bacteria | RF00005 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2) | Electron microscopy | 20 | 2014-07-09 |
| 21 | 2K4C|1|A | Transfer RNA | 76-MER | Escherichia coli | Bacteria | RF00005 | tRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS data | Solution NMR, solution scattering | 2008-12-09 |
Release history
| Release | 3.18 | 3.19 | 3.20 | 3.21 | 3.22 | 3.23 | 3.24 | 3.25 | 3.26 | 3.27 | 3.28 | 3.29 | 3.30 | 3.31 | 3.32 | 3.33 | 3.34 | 3.35 | 3.36 | 3.37 | 3.38 | 3.39 | 3.40 | 3.41 | 3.42 | 3.43 | 3.44 | 3.45 | 3.46 | 3.47 | 3.48 | 3.49 | 3.50 | 3.51 | 3.52 | 3.53 | 3.54 | 3.55 | 3.56 | 3.57 | 3.58 | 3.59 | 3.60 | 3.61 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Date | 2018-04-20 | 2018-04-27 | 2018-05-04 | 2018-05-11 | 2018-05-18 | 2018-05-25 | 2018-06-01 | 2018-06-08 | 2018-06-15 | 2018-06-22 | 2018-06-29 | 2018-07-06 | 2018-07-13 | 2018-07-20 | 2018-07-27 | 2018-08-03 | 2018-08-10 | 2018-08-17 | 2018-08-24 | 2018-08-31 | 2018-09-07 | 2018-09-14 | 2018-09-21 | 2018-09-28 | 2018-10-05 | 2018-10-12 | 2018-10-19 | 2018-10-26 | 2018-11-02 | 2018-11-09 | 2018-11-16 | 2018-11-23 | 2018-11-30 | 2018-12-07 | 2018-12-14 | 2018-12-21 | 2018-12-28 | 2019-01-04 | 2019-01-11 | 2019-01-18 | 2019-01-25 | 2019-02-01 | 2019-02-08 | 2019-02-15 |
Parents
| This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
|---|---|---|---|---|---|
| NR_all_69813.3 | NR_all_69813.2 | 3.18 | (17) 4V77|1|A1, 4V6Z|1|A1, 4V76|1|A1, 4V6Y|1|A1, 4V75|1|A1, 5IBB|1|3L, 2K4C|1|A, 4V74|1|A1, 5IBB|1|3K, 4V73|1|A1, 5IBB|1|1K, 4V72|1|A1, 4V7A|1|A1, 4V71|1|A1, 4V79|1|A1, 4V78|1|A1, 4V70|1|A1 | (4) 6CAE|1|2w, 6CAE|1|1y, 6CAE|1|1w, 6CAE|1|2y | (0) |
Children
| This class | Descendant classes | Release id | Intersection | Only in this class | Added to child |
|---|---|---|---|---|---|
| NR_all_69813.3 | NR_all_69813.4 | 3.62 | (21) 4V6Y|1|A1, 4V72|1|A1, 4V76|1|A1, 4V7A|1|A1, 6CAE|1|1w, 6CAE|1|2y, 2K4C|1|A, 4V71|1|A1, 4V75|1|A1, 4V79|1|A1, 5IBB|1|3L, 4V70|1|A1, 4V74|1|A1, 4V78|1|A1, 5IBB|1|3K, 6CAE|1|2w, 4V6Z|1|A1, 4V73|1|A1, 4V77|1|A1, 5IBB|1|1K, 6CAE|1|1y | (0) | (4) 6ND6|1|1y, 6ND6|1|1w, 6ND6|1|2y, 6ND6|1|2w |
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 | 4V7A|1|A1 | E. coli 70S-fMetVal-tRNAVal post-translocation complex (post4) | ELECTRON MICROSCOPY | 9 | 70 |
| 2 | 4V76|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2a) | ELECTRON MICROSCOPY | 17 | 70 |
| 3 | 4V79|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3b) | ELECTRON MICROSCOPY | 15 | 70 |
| 4 | 4V78|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post3a) | ELECTRON MICROSCOPY | 20 | 70 |
| 5 | 6CAE|1|2y | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-RAY DIFFRACTION | 2.6 | 67 |
| 6 | 6CAE|1|1y | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-RAY DIFFRACTION | 2.6 | 68 |
| 7 | 5IBB|1|3L | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-RAY DIFFRACTION | 2.96 | 71 |
| 8 | 5IBB|1|3K | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-RAY DIFFRACTION | 2.96 | 70 |
| 9 | 4V72|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre4) | ELECTRON MICROSCOPY | 13 | 70 |
| 10 | 4V73|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5a) | ELECTRON MICROSCOPY | 15 | 70 |
| 11 | 4V6Z|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1b) | ELECTRON MICROSCOPY | 12 | 70 |
| 12 | 4V71|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre2) | ELECTRON MICROSCOPY | 20 | 70 |
| 13 | 4V74|1|A1 | 70S-fMetVal-tRNAVal-tRNAfMet complex in hybrid pre-translocation state (pre5b) | ELECTRON MICROSCOPY | 17 | 70 |
| 14 | 5IBB|1|1K | Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site | X-RAY DIFFRACTION | 2.96 | 67 |
| 15 | 4V70|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate pre-translocation state (pre3) | ELECTRON MICROSCOPY | 17 | 70 |
| 16 | 4V6Y|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic pre-translocation state (pre1a) | ELECTRON MICROSCOPY | 12 | 70 |
| 17 | 6CAE|1|2w | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-RAY DIFFRACTION | 2.6 | 67 |
| 18 | 6CAE|1|1w | Crystal structure of the Thermus thermophilus 70S ribosome in complex with NOSO-95179 antibiotic and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution | X-RAY DIFFRACTION | 2.6 | 67 |
| 19 | 4V75|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in classic post-translocation state (post1) | ELECTRON MICROSCOPY | 12 | 70 |
| 20 | 4V77|1|A1 | E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b) | ELECTRON MICROSCOPY | 17 | 70 |
| 21 | 2K4C|1|A | tRNAPhe-based homology model for tRNAVal refined against base N-H RDCs in two media and SAXS data | SOLUTION NMR, SOLUTION SCATTERING | 76 |