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

  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},
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

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.

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.

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

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*

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.

Tertiary core rearrangements in a tight binding transfer RNA aptamer.

The engineered tRNA mutant 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.

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

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.

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

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



Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

The crystal structure of the RNA-binding domain of the small nuclear ribonucleoprotein U1A bound to a 21-nucleotide RNA hairpin has been determined and reveals the stereochemical basis for sequence-specific RNA recognition by the RNP domain.

The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.

Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution using chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids.

Crystal structure of an RNA bacteriophage coat protein–operator complex

The crystal structure at 3.0 Å resolution of a complex between recombinant MS2 cap-sids and the 19-nucleotide RNA fragment is reported, the first example of a structure at this resolution for a sequence-specific protein-RNA complex apart from the transfer RNA synthetase complexes.

The refined structure of bacteriophage MS2 at 2.8 A resolution.

The extensive dimer contact supports the idea of dimers as initial building blocks and an assembly pathway is proposed where five dimers converge into a pentamer and 12 pentamers are linked together with free dimers creating a complete particle.

An RNA mutation that increases the affinity of an RNA-protein interaction.

The introduction of a cytidine in place of one of the two single stranded uridines in the R17 replicase translational operator results in a much tighter binding to R17 coat protein. The complex

Probing sequence-specific RNA recognition by the bacteriophage MS2 coat protein

The results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein confirm that the complexes which form between TR and RNA-free phage capsids are identical to those which form in solution betweenTR and a single coat protein dimer.

The RNA-binding Site of Bacteriophage Qβ Coat Protein*

The results of these and other studies indicate that, although they bind different RNAs, the binding sites of the two coat proteins are sufficiently similar that each is easily converted by mutation to the RNA binding specificity of the other.

Deep penetration of an α-helix into a widened RNA major groove in the HIV-1 rev peptide–RNA aptamer complex

The details of molecular recognition associated with targeting by rev of a HIV-117-mer rev peptide bound to its 35-mer high affinity RNA aptamer binding site open new opportunities for structure-based drug design strategies.

Structure, recognition and adaptive binding in RNA aptamer complexes.

A comparative analysis of the structures of these RNA aptamer complexes yields the principles, patterns and diversity associated with RNA architecture, molecular recognition and adaptive binding associated with complex formation.