1ZDH

MS2 COAT PROTEIN/RNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

Valegard, K.Murray, J.B.Stonehouse, N.J.van den Worm, S.Stockley, P.G.Liljas, L.

(1997) J.Mol.Biol. 270: 724-738

  • DOI: 10.1006/jmbi.1997.1144
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect th ...

    Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.


    Related Citations: 
    • Crystal Structure of an RNA Bacteriophage Coat Protein-Operator Complex
      Valegard, K.,Murray, J.B.,Stockley, P.G.,Stonehouse, N.J.,Liljas, L.
      (1994) Nature 371: 623
    • The Refined Structure of Bacteriophage MS2 at 2.8 A Resolution
      Golmohammadi, R.,Valegard, K.,Fridborg, K.,Liljas, L.
      (1993) J.Mol.Biol. 234: 620


    Organizational Affiliation

    Department of Molecular Biology, Uppsala University, Uppsala, Box 590, S-751 24, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (BACTERIOPHAGE MS2 COAT PROTEIN)
A, B, C
129Escherichia phage MS2Mutation(s): 0 
Find proteins for P03612 (Escherichia phage MS2)
Go to UniProtKB:  P03612
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*U P*GP*U)-3')R,S19synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Work: 0.186 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 288.000α = 90.00
b = 288.000β = 90.00
c = 653.000γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-02-15
    Type: Source and taxonomy, Structure summary