4MGU | pdb_00004mgu

Crystal structure of Acheta domesticus Densovirus

• PDB DOI: https://doi.org/10.2210/pdb4MGU/pdb
• NAKB: 4MGU

• Classification: VIRUS/DNA
• Organism(s): Acheta domestica densovirus, Acheta domesticus
• Mutation(s): No 


• Deposited: 2013-08-28 Released: 2013-10-30 
• Deposition Author(s): Meng, G., Rossmann, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.290 (Depositor), 0.305 (DCC) 
• R-Value Observed: 
  0.290 (Depositor) 

Literature

The structure and host entry of an invertebrate parvovirus.

Meng, G., Zhang, X., Plevka, P., Yu, Q., Tijssen, P., Rossmann, M.G.

(2013) J Virol 87: 12523-12530

• PubMed: 24027306 
• DOI: https://doi.org/10.1128/JVI.01822-13
• Primary Citation Related Structures: 
  4MGU


• PubMed Abstract: 
  

  The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome.

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Organizational Affiliation: 
• Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.

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: 47.72 kDa 
• Atom Count: 3,005 
• Modeled Residue Count: 382 
• Deposited Residue Count: 431 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural protein VP2	A	428	Acheta domestica densovirus	Mutation(s): 0
UniProt
Find proteins for F2Y986 (Acheta domestica densovirus) Explore F2Y986  Go to UniProtKB:  F2Y986

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*T)-3')	B [auth C]	3	Acheta domesticus

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.290 (Depositor), 0.305 (DCC) 
• R-Value Observed: 0.290 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 415.469	α = 90
b = 415.469	β = 90
c = 281.93	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
GLRF	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-30 
Deposition Author(s): Meng, G., Rossmann, M.G.

Revision History  

• Version 1.0: 2013-10-30
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Database references
• Version 1.2: 2013-12-18
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations