1XOK

crystal structure of alfalfa mosaic virus RNA 3'UTR in complex with coat protein N terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cofolding organizes alfalfa mosaic virus RNA and coat protein for replication.

Guogas, L.M.Filman, D.J.Hogle, J.M.Gehrke, L.

(2004) Science 306: 2108-2111

  • DOI: 10.1126/science.1103399
  • Primary Citation of Related Structures:  
    1XOK

  • PubMed Abstract: 
  • Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting ...

    Alfalfa mosaic virus genomic RNAs are infectious only when the viral coat protein binds to the RNA 3' termini. The crystal structure of an alfalfa mosaic virus RNA-peptide complex reveals that conserved AUGC repeats and Pro-Thr-x-Arg-Ser-x-x-Tyr coat protein amino acids cofold upon interacting. Alternating AUGC residues have opposite orientation, and they base pair in different adjacent duplexes. Localized RNA backbone reversals stabilized by arginine-guanine interactions place the adenosines and guanines in reverse order in the duplex. The results suggest that a uniform, organized 3' conformation, similar to that found on viral RNAs with transfer RNA-like ends, may be essential for replication.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA 02115, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Coat proteinC, D26N/AMutation(s): 0 
UniProt
Find proteins for P24264 (Alfalfa mosaic virus (strain YSMV))
Explore P24264 
Go to UniProtKB:  P24264
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
alfalfa mosaic virus RNA 3' UTRA30N/A
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    alfalfa mosaic virus RNA 3' UTRB9N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    BR
    Query on BR

    Download Ideal Coordinates CCD File 
    E [auth A]BROMIDE ION
    Br
    CPELXLSAUQHCOX-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.269 
    • R-Value Work: 0.249 
    • R-Value Observed: 0.251 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 50.1α = 90
    b = 123β = 90
    c = 53.6γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement
    HKL-2000data reduction
    SCALEPACKdata scaling
    SHARPphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2005-01-04
      Type: Initial release
    • Version 1.1: 2008-04-30
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Advisory, Refinement description, Version format compliance