4AGJ

Crystal structure of the capsid protein (110-267) from Aura virus in complex with dioxane


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 interact ...

    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 67: 1394


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAPSID PROTEIN
A
158Aura virusMutation(s): 0 
Find proteins for Q86925 (Aura virus)
Go to UniProtKB:  Q86925
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DIO
Query on DIO

Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.434α = 90.00
b = 35.425β = 101.67
c = 49.171γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references
  • Version 1.2: 2015-03-25
    Type: Database references