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 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 

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

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coat protein
C, D
26Alfalfa mosaic virus (strain YSMV)N/A
Find proteins for P24264 (Alfalfa mosaic virus (strain YSMV))
Go to UniProtKB:  P24264
Entity ID: 1
MoleculeChainsLengthOrganism
alfalfa mosaic virus RNA 3' UTRA30N/A
Entity ID: 2
MoleculeChainsLengthOrganism
alfalfa mosaic virus RNA 3' UTRB9N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR

Download SDF File 
Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.249 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.100α = 90.00
b = 123.000β = 90.00
c = 53.600γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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