1U1Y

Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2aminopurine substituted at the-10 position


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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.

Horn, W.T.Convery, M.A.Stonehouse, N.J.Adams, C.J.Liljas, L.Phillips, S.E.Stockley, P.G.

(2004) RNA 10: 1776-1782

  • DOI: 10.1261/rna.7710304
  • Primary Citation of Related Structures:  
    1U1Y

  • PubMed Abstract: 
  • We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein ...

    We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. 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. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.


    Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coat proteinC [auth A], D [auth B], E [auth C]129Escherichia phage MS2Mutation(s): 0 
UniProt
Find proteins for P03612 (Escherichia phage MS2)
Explore P03612 
Go to UniProtKB:  P03612
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*CP*CP*GP*GP*(2PR)P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'A [auth R], B [auth S]17N/A
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.85 Å
    • R-Value Free: 0.196 
    • R-Value Work: 0.188 
    • R-Value Observed: 0.188 
    • Space Group: H 3 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 288.61α = 90
    b = 288.61β = 90
    c = 654.68γ = 120
    Software Package:
    Software NamePurpose
    MOSFLMdata reduction
    SCALAdata scaling
    X-PLORmodel building
    X-PLORrefinement
    CCP4data scaling
    X-PLORphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2004-12-07
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance