Experimental Data Snapshot

  • Resolution: 2.38 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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

Grahn, E.Moss, T.Helgstrand, C.Fridborg, K.Sundaram, M.Tars, K.Lago, H.Stonehouse, N.J.Davis, D.R.Stockley, P.G.Liljas, L.

(2001) RNA 7: 1616-1627

  • Primary Citation of Related Structures:  
    2BU1, 2C4Q, 2C4Y, 2C4Z, 2C50, 2C51

  • PubMed Abstract: 

    We have determined the X-ray structures of six MS2 RNA hairpin-coat-protein complexes having five different substitutions at the hairpin loop base -5. This is a uracil in the wild-type hairpin and contacts the coat protein both by stacking on to a tyrosine side chain and by hydrogen bonding to an asparagine side chain. The RNA consensus sequence derived from coat protein binding studies with natural sequence variants suggested that the -5 base needs to be a pyrimidine for strong binding. The five -5 substituents used in this study were 5-bromouracil, pyrimidin-2-one, 2-thiouracil, adenine, and guanine. The structure of the 5-bromouracil complex was determined to 2.2 A resolution, which is the highest to date for any MS2 RNA-protein complex. All the complexes presented here show very similar conformations, despite variation in affinity in solution. The results suggest that the stacking of the -5 base on to the tyrosine side chain is the most important driving force for complex formation. A number of hydrogen bonds that are present in the wild-type complex are not crucial for binding, as they are missing in one or more of the complexes. The results also reveal the flexibility of this RNA-protein interface, with respect to functional group variation, and may be generally applicable to other RNA-protein complexes.

  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Sweden.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
129Escherichia phage MS2Mutation(s): 0 
Find proteins for P03612 (Escherichia phage MS2)
Explore P03612 
Go to UniProtKB:  P03612
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03612
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
E [auth S]
19Escherichia phage MS2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.38 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288α = 90
b = 288β = 90
c = 653γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-07
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description