Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 32.38 kDa 
• Atom Count: 1,902 
• Modelled Residue Count: 224 
• Deposited Residue Count: 259 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 4FVU

Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease

• PDB DOI:  https://doi.org/10.2210/pdb4FVU/pdb
• NDB: NA1940

• Classification: HYDROLASE/RNA
• Organism(s): Lassa virus Josiah, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-29 Released: 2012-09-19 
• Deposition Author(s): Hastie, K.M., King, L.B., Zandonatti, M.A., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.254 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 

Literature

Structural Basis for the dsRNA Specificity of the Lassa Virus NP Exonuclease.

Hastie, K.M., King, L.B., Zandonatti, M.A., Saphire, E.O.

(2012) PLoS One 7: e44211-e44211

• PubMed: 22937163 
• DOI: https://doi.org/10.1371/journal.pone.0044211
• Primary Citation of Related Structures:  
  4FVU


• PubMed Abstract: 
  

Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA). dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by "relocation" of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.

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Organizational Affiliation: 

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A	243	Lassa virus Josiah	Mutation(s): 1  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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*GP*GP*GP*AP*G)-3')	B	8	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*UP*CP*CP*CP*UP*CP*C)-3')	C	8	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.254 
• R-Value Work: 0.197 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.772	α = 90
b = 84.311	β = 90
c = 79.809	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Hastie, K.M., King, L.B., Zandonatti, M.A., Saphire, E.O.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2018-03-14
  Changes: Database references
• Version 1.3: 2018-06-20
  Changes: Data collection