Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.43 kDa 
• Atom Count: 1840 
• Modelled Residue Count: 207 
• Deposited Residue Count: 243 
• Unique protein chains: 1

3Q7B

Exonuclease domain of Lassa virus nucleoprotein

• PDB DOI: 10.2210/pdb3Q7B/pdb

• Classification: HYDROLASE
• Organism(s): Lassa virus Josiah
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-02-09 
• Deposition Author(s): Hastie, K.M., Kimberlin, C.R., Zandonatti, M.A., MacRae, I.J., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 

Literature

Structure of the Lassa virus nucleoprotein reveals a dsRNA-specific 3' to 5' exonuclease activity essential for immune suppression.

Hastie, K.M., Kimberlin, C.R., Zandonatti, M.A., Macrae, I.J., Saphire, E.O.

(2011) Proc Natl Acad Sci U S A 108: 2396-2401

• PubMed: 21262835 
• DOI: 10.1073/pnas.1016404108
• Primary Citation of Related Structures:  
  3Q7B, 3Q7C


• PubMed Abstract: 
  

Lassa fever virus, a member of the family Arenaviridae, is a highly endemic category A pathogen that causes 300,000-500,000 infections per year in Western Africa. The arenaviral nucleoprotein NP has been implicated in suppression of the host innate immune system, but the mechanism by which this occurs has remained elusive. Here we present the crystal structure at 1.5 Å of the immunosuppressive C-terminal portion of Lassa virus NP and illustrate that, unexpectedly, its 3D fold closely mimics that of the DEDDh family of exonucleases. Accompanying biochemical experiments illustrate that NP indeed has a previously unknown, bona fide exonuclease activity, with strict specificity for double-stranded RNA substrates. We further demonstrate that this exonuclease activity is essential for the ability of NP to suppress translocation of IFN regulatory factor 3 and block activation of the innate immune system. Thus, the nucleoprotein is a viral exonuclease with anti-immune activity, and this work provides a unique opportunity to combat arenaviral infections.

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Organizational Affiliation: 

Departments of Immunology and Microbial Science and Molecular Biology, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	243	Lassa virus Josiah	Mutation(s): 0  Gene Names: N EC: 3.1.13
UniProt
Find proteins for P13699 (Lassa virus (strain Mouse/Sierra Leone/Josiah/1976)) Explore P13699  Go to UniProtKB:  P13699

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.189 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.998	α = 90
b = 68.233	β = 90
c = 79.006	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-04 
• Released Date: 2011-02-09 
Deposition Author(s): Hastie, K.M., Kimberlin, C.R., Zandonatti, M.A., MacRae, I.J., Saphire, E.O.

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance