4O6I | pdb_00004o6i

2.0A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain

• PDB DOI: https://doi.org/10.2210/pdb4O6I/pdb

• Classification: HYDROLASE
• Organism(s): Lymphocytic choriomeningitis virus (strain Armstrong)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-20 Released: 2014-06-11 
• Deposition Author(s): West, B.R., Hastie, K.M., Saphire, E.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structure of the LCMV nucleoprotein provides a template for understanding arenavirus replication and immunosuppression.

West, B.R., Hastie, K.M., Saphire, E.O.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1764-1769

• PubMed: 24914986 
• DOI: https://doi.org/10.1107/S1399004714007883
• Primary Citation of Related Structures:  
  4O6H, 4O6I


• PubMed Abstract: 
  

  The X-ray crystal structure of the Lymphocytic choriomeningitis virus nucleoprotein C-terminal immunosuppressive domain (LCMV NPΔ340) was determined to 2.0 Å resolution. The structure indicates that LCMV NPΔ340, like the other structurally characterized arenaviral nucleoproteins, adopts the fold of an exonuclease. This structure provides a crucial three-dimensional template for functional exploration of the replication and immunosuppression of this prototypic arenavirus.

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Organizational Affiliation: 

Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 53.67 kDa 
• Atom Count: 3,394 
• Modelled Residue Count: 406 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B	233	Lymphocytic choriomeningitis virus (strain Armstrong)	Mutation(s): 0  Gene Names: N EC: 3.1.13
UniProt
Find proteins for P09992 (Lymphocytic choriomeningitis virus (strain Armstrong)) Explore P09992  Go to UniProtKB:  P09992

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.962	α = 90
b = 89.962	β = 90
c = 145.941	γ = 120

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-11 
Deposition Author(s): West, B.R., Hastie, K.M., Saphire, E.O.

Revision History  

• Version 1.0: 2014-06-11
  Type: Initial release
  
• Version 1.1: 2014-07-02
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description