Equivalence class NR_2.5_56726.125 Obsolete
# | IFE | Standardized name | Molecule | Organism | Source | Rfam | Title | Method | Res. Å | #NTs | Date |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | 4YBB|1|AA (rep) | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 1534 | 2015-03-18 |
2 | 4YBB|1|BA | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | High-resolution structure of the Escherichia coli ribosome | X-ray diffraction | 2.1 | 1533 | 2015-03-18 |
3 | 8B0X|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli B | Bacteria | RF00177 | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | Electron microscopy | 1.55 | 1500 | 2022-11-30 |
4 | 8FTO|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome with an improved MS2 tag inserted in H98 | Electron microscopy | 1.85 | 1519 | 2023-08-02 |
5 | 8AYE|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | Electron microscopy | 1.96 | 1519 | 2023-03-01 |
6 | 7K00|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | Electron microscopy | 1.98 | 1519 | 2020-09-23 |
7 | 8QOA|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Structure of SecM-stalled Escherichia coli 70S ribosome | Electron microscopy | 2 | 1513 | 2024-03-20 |
8 | 8G6W|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe | Electron microscopy | 2.02 | 1519 | 2023-04-05 |
9 | 8BIM|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site | Electron microscopy | 2.04 | 1534 | 2023-08-16 |
10 | 8BIL|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | Initiation complex of the E. coli 70S ribosome with mRNA containing AAA codon in the A-site. | Electron microscopy | 2.04 | 1534 | 2023-08-16 |
11 | 8EMM|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates | Electron microscopy | 2.1 | 1519 | 2023-05-31 |
12 | 8QBT|1|i | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | E. coli ApdP-stalled ribosomal complex | Electron microscopy | 2.2 | 1539 | 2024-03-20 |
13 | 8BGE|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and AAm6A mRNA codon in the A-site after uncompleted di-peptide formation | Electron microscopy | 2.11 | 1534 | 2023-08-16 |
14 | 8R6C|1|A | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00177 | 70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA. | Electron microscopy | 2.2 | 1519 | 2024-07-24 |
15 | 8EIU|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | Electron microscopy | 2.24 | 1519 | 2023-02-01 |
16 | 8BF7|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | 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 | 1534 | 2023-08-16 |
17 | 7S1H|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli ribosome with antibiotic linezolid | Electron microscopy | 2.35 | 1540 | 2021-11-17 |
18 | 7N1P|1|16 | Small subunit ribosomal RNA | 16S rRNA, mRNA | Escherichia coli K-12 | Bacteria | RF00177 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | Electron microscopy | 2.33 | 1542 | 2021-07-14 |
19 | 8AKN|1|B | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00177 | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | Electron microscopy | 2.3 | 1519 | 2023-03-08 |
20 | 8BHL|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and Am6AA mRNA codon in the A-site after uncompleted di-peptide formation | Electron microscopy | 2.21 | 1534 | 2023-08-16 |
21 | 8HSP|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state | Electron microscopy | 2.32 | 1519 | 2024-04-03 |
22 | 7Y7G|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) | Electron microscopy | 2.34 | 1520 | 2023-10-25 |
23 | 7S1K|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.42 | 1540 | 2022-01-19 |
24 | 9FBV|1|A | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00177 | 70S Escherichia coli ribosome with P-site initiatior tRNA. | Electron microscopy | 2.4 | 1519 | 2024-06-26 |
25 | 8R8M|1|A | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli BW25113 | Bacteria | RF00177 | 70S Escherichia coli ribosome with Paenilamicin B2 bound with hybrid A/P- and hybrid P/E-tRNA. | Electron microscopy | 2.4 | 1519 | 2024-07-24 |
26 | 7S1J|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli ribosome with antibiotic radezolid | Electron microscopy | 2.47 | 1540 | 2022-03-02 |
27 | 8HTZ|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state | Electron microscopy | 2.4 | 1519 | 2024-04-03 |
28 | 7O1A|1|AA | Small subunit ribosomal RNA | Ribosomal RNA 16S | Escherichia coli K-12 | Bacteria | RF00177 | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | Electron microscopy | 2.4 | 1534 | 2021-09-01 |
29 | 7S1I|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | Electron microscopy | 2.48 | 1540 | 2022-03-02 |
30 | 7S1G|1|C | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | Electron microscopy | 2.48 | 1540 | 2021-11-17 |
31 | 7Y7E|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU) | Electron microscopy | 2.41 | 1520 | 2023-10-25 |
32 | 7Y7F|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli | Bacteria | RF00177 | Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAC) | Electron microscopy | 2.43 | 1520 | 2023-10-25 |
33 | 8IFB|1|A | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli | Bacteria | RF00177 | Dibekacin-bound E.coli 70S ribosome in the PURE system | Electron microscopy | 2.43 | 1519 | 2024-02-14 |
34 | 8BHP|1|2 | Small subunit ribosomal RNA | 16S rRNA RRSB-RRNA | Escherichia coli K-12 | Bacteria | RF00177 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and m6AAA mRNA codon in the A-site after uncompleted di-peptide formation | Electron microscopy | 2.37 | 1534 | 2023-08-16 |
35 | 8CGJ|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Streptomycin bound to the 30S body | Electron microscopy | 1.79 | 1130 | 2023-07-26 |
36 | 8CGU|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Gentamicin bound to the 30S body | Electron microscopy | 1.89 | 1047 | 2023-07-26 |
37 | 8CAI|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Streptomycin and Hygromycin B bound to the 30S body | Electron microscopy | 2.08 | 1114 | 2023-07-26 |
38 | 8CEP|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Round2 30S head (no antibiotic) | Electron microscopy | 2.04 | 1046 | 2023-07-19 |
39 | 8CGR|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Apramycin bound to the 30S body | Electron microscopy | 2.12 | 1060 | 2023-07-26 |
40 | 8CF1|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Tetracycline bound to the 30S head | Electron microscopy | 1.82 | 485 | 2023-07-26 |
41 | 7PJS|1|a | Small subunit ribosomal RNA | 16S ribosomal RNA | Escherichia coli | Bacteria | RF00177 | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | Electron microscopy | 2.35 | 662 | 2021-10-20 |
42 | 8CGI|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Pentacycline TP038 bound to the 30S head | Electron microscopy | 1.89 | 460 | 2023-07-26 |
43 | 8CA7|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Omadacycline and spectinomycin bound to the 30S ribosomal subunit head | Electron microscopy | 2.06 | 502 | 2023-08-02 |
44 | 8CAZ|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | empty 30S head | Electron microscopy | 2.11 | 460 | 2023-07-26 |
45 | 8CF8|1|A | Small subunit ribosomal RNA | 16S rRNA | Escherichia coli BW25113 | Bacteria | RF00177 | Eravacycline bound to the 30S head | Electron microscopy | 2.2 | 460 | 2023-08-02 |
Parents
This class | Parent classes | Release id | Intersection | Added to this class | Only in parent |
---|
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 | View | PDB | Title | Method | Resolution | #NTs |
---|---|---|---|---|---|---|
1 | 8BF7|1|2 | 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 | 1534 | |
2 | 8BHL|1|2 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and Am6AA mRNA codon in the A-site after uncompleted di-peptide formation | ELECTRON MICROSCOPY | 2.21 | 1534 | |
3 | 8BGE|1|2 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and AAm6A mRNA codon in the A-site after uncompleted di-peptide formation | ELECTRON MICROSCOPY | 2.11 | 1534 | |
4 | 8BIL|1|2 | Initiation complex of the E. coli 70S ribosome with mRNA containing AAA codon in the A-site. | ELECTRON MICROSCOPY | 2.04 | 1534 | |
5 | 8BHP|1|2 | Elongating E. coli 70S ribosome containing acylated tRNA(iMet) in the P-site and m6AAA mRNA codon in the A-site after uncompleted di-peptide formation | ELECTRON MICROSCOPY | 2.37 | 1534 | |
6 | 8BIM|1|2 | Initiation complex of the E. coli 70S ribosome with mRNA containing AAm6A codon in the A-site | ELECTRON MICROSCOPY | 2.04 | 1534 | |
7 | 7O1A|1|AA | Cryo-EM structure of an Escherichia coli TnaC(R23F)-ribosome complex stalled in response to L-tryptophan | ELECTRON MICROSCOPY | 2.4 | 1534 | |
8 | 8B0X|1|A | Translating 70S ribosome in the unrotated state (P and E, tRNAs) | ELECTRON MICROSCOPY | 1.55 | 1500 | |
9 | 7S1J|1|C | Wild-type Escherichia coli ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.47 | 1540 | |
10 | 7S1K|1|C | Cfr-modified Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.42 | 1540 | |
11 | 7S1H|1|C | Wild-type Escherichia coli ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.35 | 1540 | |
12 | 7S1G|1|C | wild-type Escherichia coli stalled ribosome with antibiotic linezolid | ELECTRON MICROSCOPY | 2.48 | 1540 | |
13 | 7S1I|1|C | Wild-type Escherichia coli stalled ribosome with antibiotic radezolid | ELECTRON MICROSCOPY | 2.48 | 1540 | |
14 | 8QOA|1|A | Structure of SecM-stalled Escherichia coli 70S ribosome | ELECTRON MICROSCOPY | 2 | 1513 | |
15 | 8FTO|1|A | E. coli 70S ribosome with an improved MS2 tag inserted in H98 | ELECTRON MICROSCOPY | 1.85 | 1519 | |
16 | 8AYE|1|A | E. coli 70S ribosome bound to thermorubin and fMet-tRNA | ELECTRON MICROSCOPY | 1.96 | 1519 | |
17 | 9FBV|1|A | 70S Escherichia coli ribosome with P-site initiatior tRNA. | ELECTRON MICROSCOPY | 2.4 | 1519 | |
18 | 8AKN|1|B | Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome | ELECTRON MICROSCOPY | 2.3 | 1519 | |
19 | 8CGR|1|A | Apramycin bound to the 30S body | ELECTRON MICROSCOPY | 2.12 | 1060 | |
20 | 8CEP|1|A | Round2 30S head (no antibiotic) | ELECTRON MICROSCOPY | 2.04 | 1046 | |
21 | 8CGU|1|A | Gentamicin bound to the 30S body | ELECTRON MICROSCOPY | 1.89 | 1047 | |
22 | 4YBB|1|BA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 1533 | |
23 | 8CAI|1|A | Streptomycin and Hygromycin B bound to the 30S body | ELECTRON MICROSCOPY | 2.08 | 1114 | |
24 | 7PJS|1|a | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | ELECTRON MICROSCOPY | 2.35 | 662 | |
25 | 4YBB|1|AA | High-resolution structure of the Escherichia coli ribosome | X-RAY DIFFRACTION | 2.1 | 1534 | |
26 | 8CGJ|1|A | Streptomycin bound to the 30S body | ELECTRON MICROSCOPY | 1.79 | 1130 | |
27 | 8R6C|1|A | 70S Escherichia coli ribosome with Paenilamicin B2 bound with A- and P-site tRNA. | ELECTRON MICROSCOPY | 2.2 | 1519 | |
28 | 8EMM|1|A | Composite 70S ribosome structure for "Atomistic simulations of the E. coli ribosome provide selection criteria for translationally active substrates | ELECTRON MICROSCOPY | 2.1 | 1519 | |
29 | 7K00|1|A | Structure of the Bacterial Ribosome at 2 Angstrom Resolution | ELECTRON MICROSCOPY | 1.98 | 1519 | |
30 | 8G6W|1|A | Structure of WT E.coli 70S ribosome complexed with mRNA, P-site fMet-NH-tRNAfMet and A-site ortho-aminobenzoic acid charged NH-tRNAPhe | ELECTRON MICROSCOPY | 2.02 | 1519 | |
31 | 8IFB|1|A | Dibekacin-bound E.coli 70S ribosome in the PURE system | ELECTRON MICROSCOPY | 2.43 | 1519 | |
32 | 8EIU|1|A | E. coli 70S ribosome with A-loop mutations U2554C and U2555C | ELECTRON MICROSCOPY | 2.24 | 1519 | |
33 | 8HTZ|1|A | E. coli 70S ribosome complexed with H. marismortui tRNA_Ile2 bearing agm2C34 in classical state | ELECTRON MICROSCOPY | 2.4 | 1519 | |
34 | 8HSP|1|A | E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state | ELECTRON MICROSCOPY | 2.32 | 1519 | |
35 | 7Y7G|1|A | Structure of the Bacterial Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) | ELECTRON MICROSCOPY | 2.34 | 1520 | |
36 | 7Y7E|1|A | Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU) | ELECTRON MICROSCOPY | 2.41 | 1520 | |
37 | 7Y7F|1|A | Structure of the Bacterial Ribosome with human tRNA Asp(ManQ34) and mRNA(GAC) | ELECTRON MICROSCOPY | 2.43 | 1520 | |
38 | 7N1P|1|16 | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ELECTRON MICROSCOPY | 2.33 | 1542 | |
39 | 8QBT|1|i | E. coli ApdP-stalled ribosomal complex | ELECTRON MICROSCOPY | 2.2 | 1539 | |
40 | 8R8M|1|A | 70S Escherichia coli ribosome with Paenilamicin B2 bound with hybrid A/P- and hybrid P/E-tRNA. | ELECTRON MICROSCOPY | 2.4 | 1519 | |
41 | 8CF1|1|A | Tetracycline bound to the 30S head | ELECTRON MICROSCOPY | 1.82 | 485 | |
42 | 8CGI|1|A | Pentacycline TP038 bound to the 30S head | ELECTRON MICROSCOPY | 1.89 | 460 | |
43 | 8CAZ|1|A | empty 30S head | ELECTRON MICROSCOPY | 2.11 | 460 | |
44 | 8CF8|1|A | Eravacycline bound to the 30S head | ELECTRON MICROSCOPY | 2.2 | 460 | |
45 | 8CA7|1|A | Omadacycline and spectinomycin bound to the 30S ribosomal subunit head | ELECTRON MICROSCOPY | 2.06 | 502 |
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.
Coloring options: