Crystal structure of an RNA aptamer–protein complex at 2.8 Å resolution

@article{Convery1998CrystalSO,
  title={Crystal structure of an RNA aptamer–protein complex at 2.8 {\AA} resolution},
  author={Maire A. Convery and Si{\^a}n Rowsell and Nicola J. Storehouse and Andrew D. Ellington and Ichira Hirao and James B. Murray and David S. Peabody and Simon E V Phillips and Peter G. Stockley},
  journal={Nature Structural Biology},
  year={1998},
  volume={5},
  pages={133-139}
}
The crystal structure, at 2.8 Å resolution, of an RNA aptamer bound to bacteriophage MS2 coat protein has been determined. It provides an opportunity to compare the interactions of MS2 coat protein and wild type operator with those of an aptamer, whose secondary structure differs from the wild type RNA in having a three-base loop (compared to a tetraloop) and an additional base pair between this loop and the sequence-specific recognition element in the stem. The RNA binds in the same location… 

Crystal structures of a series of RNA aptamers complexed to the same protein target

TLDR
Comparison of these new structures with other MS2-RNA complexes allows us to refine further the definition of the minimal recognition elements and suggests a possible application of the MS2 system for routine structure determination of small nucleic acid motifs.

Deletion of a single hydrogen bonding atom from the MS2 RNA operator leads to dramatic rearrangements at the RNA-coat protein interface.

TLDR
The 4one complex structure shows an unprecedented major conformationalchange in the loop region of the RNA, whereas there is almost no change in the conformation of the protein.

The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions.

TLDR
The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity.

Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements.

The coat protein of bacteriophage MS2 is known to bind specifically to an RNA hairpin formed within the MS2 genome. Structurally this hairpin is built up by an RNA double helix interrupted by one

Tertiary core rearrangements in a tight binding transfer RNA aptamer

TLDR
The engineered tRNA mutant engineered in which the five-nucleotide variable loop sequence 5′-44CAUUC48-3′ is replaced by 5″-44AGGU48- 3′ suggests that enhanced protein binding to a mutant globular RNA can arise from stabilization of RNA tertiary interactions rather than optimization of RNA–protein contacts.

Secondary Structure Mapping of an RNA Ligand That Has High Affinity for the MetJ Repressor Protein and Interference Modification Analysis of the Protein-RNA Complex*

TLDR
The secondary structure of an RNA aptamer, which has a high affinity for the Escherichia coli MetJ repressor protein, has been mapped using ribonucleases and with diethyl pyrocarbonate and Ethylation interference suggests that none of the phosphate groups are absolutely essential for tight binding.

Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex.

TLDR
X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5 suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation.

RNA recognition site of PP7 coat protein.

TLDR
The RNA structural requirements for binding to the coat protein of bacteriophage PP7, an RNA phage of Pseudomonas is described and it is found that tight binding to PP7 coat protein is favored by the existence of an 8 bp hairpin with a bulged purine on its 5' side separated by 4 bp from a 6 nt loop having the sequence Pu-U-A-G/U-G-Pu.

Solution structure of P22 transcriptional antitermination N peptide–box B RNA complex

TLDR
The identified intermolecular contacts account for the consequences of N peptide and boxB RNA mutations on bacteriophage transcriptional antitermination.

RNA architecture dictates the conformations of a bound peptide.

...

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