4AGK

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

PDB DOI: 10.2210/pdb4AGK/pdb

Classification: HYDROLASE
Organism(s): Aura virus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-30 Released: 2012-12-26
Deposition Author(s): Aggarwal, M., Kumar, P., Tomar, S.

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

wwPDB Validation 3D Report Full Report

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., Preeti, Siwach, A., Kumar, P., Kuhn, R.J., Tomar, S.

(2012) PLoS One 7: 51288

PubMed: 23251484 Search on PubMedSearch on PubMed Central
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. 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
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN	A	158	Aura virus	Mutation(s): 0 EC: 3.4.21.90
UniProt
Find proteins for Q86925 (Aura virus) Explore Q86925 Go to UniProtKB: Q86925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q86925
Protein Feature View Expand
Reference Sequence