4O6I

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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

  • DOI: 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NucleoproteinA, B233Lymphocytic choriomeningitis virus (strain Armstrong)Mutation(s): 0 
Gene Names: N, Segment S
EC: 3.1.13
UniProt
Find proteins for P09992 (Lymphocytic choriomeningitis virus (strain Armstrong))
Explore P09992 
Go to UniProtKB:  P09992
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09992
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
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		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.962α = 90
b = 89.962β = 90
c = 145.941γ = 120
Software Package:
Software NamePurpose
JBluIce-EPICSdata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references