1W39 | pdb_00001w39

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

• PDB DOI: https://doi.org/10.2210/pdb1W39/pdb

• Classification: VIRUS
• Organism(s): Turnip yellow mosaic virus
• Mutation(s): No 


• Deposited: 2004-07-14 Released: 2004-08-16 
• Deposition Author(s): van Roon, A.M.M., Bink, H.H.J., Plaisier, J.R., Pleij, C.W.A., Abrahams, J.P., Pannu, N.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free: 
  0.251 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

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 Biology 341: 1205

• PubMed: 15321716 
• DOI: https://doi.org/10.1016/j.jmb.2004.06.085
• Primary Citation 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. 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.

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 60.43 kDa 
• Atom Count: 4,094 
• Modeled Residue Count: 547 
• Deposited Residue Count: 567 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TURNIP YELLOW MOSAIC VIRUS EMPTY CAPSID	A, B, C	189	Turnip yellow mosaic virus	Mutation(s): 0
UniProt
Find proteins for P03608 (Turnip yellow mosaic virus) Explore P03608  Go to UniProtKB:  P03608

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.75 Å
• R-Value Free:  0.251 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 688.457	α = 90
b = 688.457	β = 90
c = 688.457	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-16 
Deposition Author(s): van Roon, A.M.M., Bink, H.H.J., Plaisier, J.R., Pleij, C.W.A., Abrahams, J.P., Pannu, N.S.

Revision History  

• 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
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description