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 

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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: https://doi.org/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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Coat protein
C, D
26N/AMutation(s): 0 
UniProt
Find proteins for P24264 (Alfalfa mosaic virus (strain YSMV))
Explore P24264 
Go to UniProtKB:  P24264
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24264
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
alfalfa mosaic virus RNA 3' UTR30N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
alfalfa mosaic virus RNA 3' UTR9N/A
Protein Feature View
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  • 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