1W39

Crystal structure of an artificial top component of turnip yellow mosaic virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of an Empty Capsid of Turnip Yellow Mosaic Virus.

Van Roon, A.M.M.Bink, H.H.J.Plaisier, J.R.Pleij, C.W.A.Abrahams, J.P.Pannu, N.S.

(2004) J Mol Biol 341: 1205

  • DOI: 10.1016/j.jmb.2004.06.085
  • Primary Citation of Related Structures:  
    1W39

  • PubMed Abstract: 
  • Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus ...

    Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.


    Related Citations: 
    • Crystal Structure of Turnip Yellow Mosaic Virus
      Canady, M.A., Larson, S.B., Day, J., McPherson, A.
      (1996) Nat Struct Biol 3: 771

    Organizational Affiliation

    Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TURNIP YELLOW MOSAIC VIRUS EMPTY CAPSID ABC189Turnip yellow mosaic virusMutation(s): 0 
Find proteins for P03608 (Turnip yellow mosaic virus)
Explore P03608 
Go to UniProtKB:  P03608
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.75 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 688.457α = 90
b = 688.457β = 90
c = 688.457γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-08-09
    Changes: Data collection
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation