1ZDI

RNA BACTERIOPHAGE MS2 COAT PROTEIN/RNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    1ZDH, 1ZDI

  • 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 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 ...

    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

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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RNA BACTERIOPHAGE MS2 COAT PROTEIN)C [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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03612
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*U P*GP*U)-3')A [auth R],
B [auth S]		19N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.202 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 288α = 90
b = 288β = 90
c = 653γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance