2FZ2 | pdb_00002fz2

Structure of Turnip Yellow Mosaic Virus at 100 K

• PDB DOI: https://doi.org/10.2210/pdb2FZ2/pdb
• NAKB: 2FZ2

• Classification: Virus/RNA
• Organism(s): Turnip yellow mosaic virus (Australian isolate)
• Expression System: Brassica rapa subsp. chinensis
• Mutation(s): Yes 


• Deposited: 2006-02-08 Released: 2006-02-21 
• Deposition Author(s): Larson, S.B., Lucas, R.W., McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.289 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.266 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

The RNA of turnip yellow mosaic virus exhibits icosahedral order.

Larson, S.B., Lucas, R.W., Greenwood, A., McPherson, A.

(2005) Virology 334: 245-254

• PubMed: 15780874 
• DOI: https://doi.org/10.1016/j.virol.2005.01.036
• Primary Citation Related Structures: 
  2FZ1, 2FZ2


• PubMed Abstract: 
  

  Difference electron density maps, based on structure factor amplitudes and experimental phases from crystals of wild-type turnip yellow mosaic virus and those of empty capsids prepared by freeze-thawing, show a large portion of the encapsidated RNA to have an icosahedral distribution. Four unique segments of base-paired, double-helical RNA, one to two turns in length, lie between 33-A and 101-A radius and are organized about either 2-fold or 5-fold icosahedral axes. In addition, single-stranded loops of RNA invade the pentameric and hexameric capsomeres where they contact the interior capsid surface. The remaining RNA, not seen in electron density maps, must serve as connecting links between these secondary structural elements and is likely icosahedrally disordered. The distribution of RNA observed crystallographically appears to be in agreement with models based on biochemical data and secondary structural analyses.

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Organizational Affiliation: 
• Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697-3900, USA.

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: 61.49 kDa 
• Atom Count: 4,122 
• Modeled Residue Count: 545 
• Deposited Residue Count: 570 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	B [auth A], C [auth B], D [auth C]	189	Turnip yellow mosaic virus (Australian isolate)	Mutation(s): 3
UniProt
Find proteins for P20125 (Turnip yellow mosaic virus (isolate Australia)) Explore P20125  Go to UniProtKB:  P20125

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*CP*C)-3'	A [auth D]	3	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.289 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.266 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 511.53	α = 90
b = 511.53	β = 90
c = 303.76	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-21 
Deposition Author(s): Larson, S.B., Lucas, R.W., McPherson, A.

Revision History  

• Version 1.0: 2006-02-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description