Biological Assembly 1  

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48279.70 
• Atom Count: 2511 
• Residue Count: 416 
• Unique protein chains: 1

4Z5V

Crystal Structure of MHV ns2 PDE Domain

• DOI: 10.2210/pdb4Z5V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Murine coronavirus (strain A59)
• Expression System: Escherichia coli


• Deposited: 2015-04-03 Released: 2016-02-10 
• Deposition Author(s): Sui, B.K., Huang, J.H., Peng, G.Q., Zhao, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.049 Å
• R-Value Free: 0.266 
• R-Value Work: 0.226 

Literature

Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation

Sui, B.K., Huang, J.H., Jha, B.K., Yin, P., Zhou, M., Fu, Z.F., Silverman, R.H., Weiss, S.R., Peng, G.Q., Zhao, L.

(2016) J.Gen.Virol. 97: 880-886

• PubMed: 26757803 
• DOI: 10.1099/jgv.0.000395


• PubMed Abstract: 
  

Prior studies have demonstrated that the mouse hepatitis virus (MHV) A59 strain ns2 protein is a member of the 2H phosphoesterase family and exhibits 2',5'-phosphodiesterase (PDE) activity. During the IFN antiviral response, ns2 cleaves 2',5'-oligoadenylate (2-5A), a key mediator of RNase L activation, thereby subverting the activation of RNase L and evading host innate immunity. However, the mechanism of 2-5A cleavage by ns2 remains unclear. Here, we present the crystal structure of the MHV ns2 PDE domain and demonstrate a PDE fold similar to that of the cellular protein, a kinase anchoring protein 7 central domain (AKAP7(CD)) and rotavirus VP3 carboxy-terminal domain. The structure displays a pair of strictly conserved HxT/Sx motifs and forms a deep, positively charged catalytic groove with β-sheets and an arginine-containing loop. These findings provide insight into the structural basis for 2-5A binding of MHV ns2.

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Organizational Affiliation: 

1​State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PRChina.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Non-structural protein 2a	A, B	208	Murine coronavirus (strain A59)	Mutation(s): 0
Find proteins for P19738 (Murine coronavirus (strain A59)) Go to UniProtKB:  P19738

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.049 Å
• R-Value Free: 0.266 
• R-Value Work: 0.226 
• Space Group: P 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 101.042	α = 90.00
b = 101.042	β = 90.00
c = 165.806	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	phasing
HKL-2000	data processing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-03 
• Released Date: 2016-02-10 
• Deposition Author(s): Sui, B.K., Huang, J.H., Peng, G.Q., Zhao, L.

Revision History 

• Version 1.0: 2016-02-10
  Type: Initial release
• Version 1.1: 2016-05-04
  Type: Database references