4AGK

Crystal structure of capsid protein (110-267) from Aura virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Aura Virus Capsid Protease and its Complex with Dioxane: New Insights Into Capsid-Glycoprotein Molecular Contacts

Aggarwal, M.Tapas, S.PreetiSiwach, A.Kumar, P.Kuhn, R.J.Tomar, S.

(2012) PLoS One 7: 51288

  • DOI: 10.1371/journal.pone.0051288
  • Primary Citation of Related Structures:  
    4AGJ, 4AGK

  • PubMed Abstract: 
  • The nucleocapsid core interaction with endodomains of glycoproteins plays a critical role in the alphavirus life cycle that is essential to virus budding. Recent cryo-electron microscopy (cryo-EM) studies provide structural insights into key interactions between capsid protein (CP) and trans-membrane glycoproteins E1 and E2 ...

    The nucleocapsid core interaction with endodomains of glycoproteins plays a critical role in the alphavirus life cycle that is essential to virus budding. Recent cryo-electron microscopy (cryo-EM) studies provide structural insights into key interactions between capsid protein (CP) and trans-membrane glycoproteins E1 and E2. CP possesses a chymotrypsin-like fold with a hydrophobic pocket at the surface responsible for interaction with glycoproteins. In the present study, crystal structures of the protease domain of CP from Aura virus and its complex with dioxane were determined at 1.81 and 1.98 Å resolution respectively. Due to the absence of crystal structures, homology models of E1 and E2 from Aura virus were generated. The crystal structure of CP and structural models of E1 and E2 were fitted into the cryo-EM density map of Venezuelan equine encephalitis virus (VEEV) for detailed analysis of CP-glycoprotein interactions. Structural analysis revealed that the E2 endodomain consists of a helix-loop-helix motif where the loop region fits into the hydrophobic pocket of CP. Our studies suggest that Cys397, Cys418 and Tyr401 residues of E2 are involved in stabilizing the structure of E2 endodomain. Density map fitting analysis revealed that Pro405, a conserved E2 residue is present in the loop region of the E2 endodomain helix-loop-helix structure and makes intermolecular hydrophobic contacts with the capsid. In the Aura virus capsid protease (AVCP)-dioxane complex structure, dioxane occupies the hydrophobic pocket on CP and structurally mimics the hydrophobic pyrollidine ring of Pro405 in the loop region of E2.


    Related Citations: 
    • Crystallization, High-Resolution Data Collection and Preliminary Crystallographic Analysis of Aura Virus Capsid Protease and its Complex with Dioxane.
      Aggarwal, M., Dhindwal, S., Pratap, S., Kuhn, R.J., Kumar, P., Tomar, S.
      (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1394

    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology, Roorkee, Roorkee, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAPSID PROTEINA158Aura virusMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for Q86925 (Aura virus)
Explore Q86925 
Go to UniProtKB:  Q86925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86925
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.661α = 90
b = 35.262β = 102.34
c = 49.578γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-30
    Changes: Database references