Primary Citation PubMed: 11340196
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Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
(2006) Nucleic Acids Res 34
PubMed: 16522645 | PubMedCentral: PMC1390688 | DOI: 10.1093/nar/gkl025
We studied all cis WC G/U basepairs in the 16S rRNA of the bacterium Thermus thermophilus ( Tt )—PDB files 1IBM, 3.31Å resolution, and 1J5E, 3.05Å ( 15 ), and in the 23S/5S rRN... structures of the archaeon Haloarcula marismortui ( Hm )—PDB files 1JJ2 and 1S72, both at 2.4 Å ( 16 ) and the bacterium Deinococcus radiodurans ( Dr )—PDB files 1KPJ and 1LNR, both at 3.10 Å ( 17 ).
Publication Year: 2006
Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae.
(2007) PLoS One 2
PubMed: 17565370 | PubMedCentral: PMC1885216 | DOI: 10.1371/journal.pone.0000517
PyMol (Delano Scientific, LLC) was used to generate this figure based on the coordinates 1IBM in the RSCN Protein Data Bank  .
Publication Year: 2007
The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.
(2008) Nucleic Acids Res 36
PubMed: 18346970 | PubMedCentral: PMC2377432 | DOI: 10.1093/nar/gkn112
In addition, all base pairs and base-stacking columns except residues A1492 and A1493 are present in these two bacterial ‘off’ states and in the bacterial ‘on’ state fo... nd in the T. thermophilus 30S ribosomal particle in complex with the cognate tRNA [PDB ID: 1IBM in ( 5 )].
Since this conformation is different from the ‘on’ states of the bacterial and H. sapiens cytoplasmic A sites with bulged-out A1492 and A1493 [PDB ID: 1IBM in ( 5 ); 2 FQN in ( 11 )], it should correspond to the ‘off’ state of the mitochondrial wild-type A site.
Publication Year: 2008
Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
(2008) EMBO J 27
PubMed: 19020518 | PubMedCentral: PMC2586802 | DOI: 10.1038/emboj.2008.243
To characterize the flipped-out base positions, the fragment from nt 1491 to nt 1497 in h44 was replaced by the corresponding nts in the X-ray structure of the Thermus thermophilus 30S subunit in the ... resence of a cognate PhetRNA Phe (PDB code: 1IBM, Ogle et al , 2001 ).
Structure based hypothesis of a mitochondrial ribosome rescue mechanism.
(2012) Biol Direct 7
PubMed: 22569235 | PubMedCentral: PMC3418547 | DOI: 10.1186/1745-6150-7-14
The conformation of the universally conserved ribosome decoding site nucleotides A-1492 and A-1493 is shown (C) in case of an empty A-site with both bases stacked (from PDB entry 1J5E [ 11 ]), (D) wit... mRNA and a cognate tRNA present in the A-site and both bases unstacked (from PDB entry 1IBM [ 12 ]) and (E) with a stop codon and a release factor present in the A-site in an intermediate state (from PDB entry 3MR8 [ 8 ]).
Coordinates of the ribosomal decoding centre (shown in blue) are taken from PDB entry 1IBM [ 11 ].
Publication Year: 2012
A structural basis for streptomycin-induced misreading of the genetic code.
(2013) Nat Commun 4
PubMed: 23322043 | PubMedCentral: PMC3552334 | DOI: 10.1038/ncomms2346
Figure 4 Conformational flexibility in the 30S decoding site a. Comparison of decoding interactions for near-cognate ASL GAG Leu 2 (data set Leu, PDB accession code 4DR6, colored as before) with cogna... e decoding interactions (PDB accession code 1IBM colored in grey 9 ) b. Data set Leu colored as before compared to PDB accession code 1N32 (30S subunit in complex with near-cognate ASL GAG Leu 2 , mRNA, and paromomycin, colored in grey 13 ).
A comparison of the placement of the near-cognate ASL GAG Leu 2 with streptomycin and the cognate ASL GAA Phe without antibiotic (PDB entry 1IBM 9 ) confirms that streptomycin stabilizes the near-cognate ASL in a cognate-like overall conformation with small local changes to accommodate the mismatch ( Fig. 4a ).
The position of bases 1407 to 1409 opposite of A1492 and A1493 is shifted upon streptomycin binding both in the absence (cyan) and presence (blue) of ASL and mRNA when compared with the apo-30S structure (grey) or the cognate decoding structure PDB accession code 1IBM (red).
Publication Year: 2013
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