3ZXA | pdb_00003zxa

Structure and Assembly of Turnip Crinkle Virus I. X-ray Crystallographic Structure Analysis at 3.2 A Resolution

• PDB DOI: https://doi.org/10.2210/pdb3ZXA/pdb

• Classification: VIRUS
• Organism(s): Turnip crinkle virus
• Mutation(s): Yes 


• Deposited: 2011-08-08 Released: 2012-02-08 
• Deposition Author(s): Hogle, J.M., Maeda, A., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å

Starting Model: other

Literature

Structure and Assembly of Turnip Crinkle Virus. I. X-Ray Crystallographic Structure Analysis at 3.2 A Resolution.

Hogle, J.M., Maeda, A., Harrison, S.C.

(1986) J Mol Biology 191: 625

• PubMed: 3806676 
• DOI: https://doi.org/10.1016/0022-2836(86)90450-x
• Primary Citation Related Structures: 
  3ZXA


• PubMed Abstract: 
  

  The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic symmetry. The structures are very closely related, especially in the subunit arm and S domain, where only small insertions and deletions and small co-ordinate shifts relate one chain to another. The P domains, although quite similar in fold, are oriented somewhat differently with respect to the S domains. Understanding of the structure of turnip crinkle virus has been important for analyzing its assembly, as described in an accompanying paper.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

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

Macromolecule Content 

• Total Structure Weight: 37.76 kDa 
• Atom Count: 2,237 
• Modeled Residue Count: 295 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN	A [auth C]	347	Turnip crinkle virus	Mutation(s): 1
UniProt
Find proteins for P06663 (Turnip crinkle virus) Explore P06663  Go to UniProtKB:  P06663

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 348.8	α = 90
b = 379.1	β = 90
c = 397.4	γ = 90

Software Package:

Software Name	Purpose
OPTRONICS	data reduction
DIGITAL	data reduction
SCAN12	data reduction
HARVARD	data scaling
COMBINE	phasing
FFT	phasing
BILDER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Hogle, J.M., Maeda, A., Harrison, S.C.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2015-03-04
  Changes: Database references
• Version 1.2: 2016-02-03
  Changes: Derived calculations
• Version 1.3: 2017-06-28
  Changes: Data collection
• Version 1.4: 2019-11-13
  Changes: Data collection, Database references
• Version 1.5: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description