1AQ3

BACTERIOPHAGE MS2 CAPSID PROTEIN/RNA COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments.

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

(1998) Nucleic Acids Res 26: 1345-1351

  • DOI: 10.1093/nar/26.5.1345
  • Primary Citation of Related Structures:  
    1AQ3, 1AQ4, 1MVA, 1MVB

  • PubMed Abstract: 

    • In MS2 assembly of phage particles results from an interaction between a coat protein dimer and a stem-loop of the RNA genome (the operator hairpin). Amino acid residues Thr45, which is universally conserved among the small RNA phages, and Thr59 are part of the specific RNA binding pocket and interact directly with the RNA; the former through a hydrogen bond, the latter through hydrophobic contacts ...

    In MS2 assembly of phage particles results from an interaction between a coat protein dimer and a stem-loop of the RNA genome (the operator hairpin). Amino acid residues Thr45, which is universally conserved among the small RNA phages, and Thr59 are part of the specific RNA binding pocket and interact directly with the RNA; the former through a hydrogen bond, the latter through hydrophobic contacts. The crystal structures of MS2 protein capsids formed by mutants Thr45Ala and Thr59Ser, both with and without the 19 nt wild-type operator hairpin bound, are reported here. The RNA hairpin binds to these mutants in a similar way to its binding to wild-type protein. In a companion paper both mutants are shown to be deficient in RNA binding in an in vivo assay, but in vitro the equilibrium dissociation constant is significantly higher than wild-type for the Thr45Ala mutant. The change in binding affinity of the Thr45Ala mutant is probably a direct consequence of removal of direct hydrogen bonds between the protein and the RNA. The properties of the Thr59Ser mutant are more difficult to explain, but are consistent with a loss of non-polar contact.

    Organizational Affiliation: 

    Department of Molecular Biology, Uppsala University, Box 590, S-751 24 Uppsala, Sweden and Department of Biology, University of Leeds, Leeds LS2 9JT, UK.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (BACTERIOPHAGE MS2 COAT PROTEIN)C [auth A],
D [auth B],
E [auth C]		129Escherichia phage MS2Mutation(s): 1 
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
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Work: 0.204 
  • 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
Agrovatadata scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Refinement description