4O6H

2.8A crystal structure of Lymphocytic Choriomeningitis Virus Nucleoprotein C-terminal Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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.

    • 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
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoprotein
A, B, C, D, E
A, B, C, D, E, F, G, H
233Lymphocytic choriomeningitis virus (strain Armstrong)Mutation(s): 0 
Gene Names: N
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
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD
Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
T [auth E],
V [auth F]		IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
P [auth D]
S [auth E]
I [auth A],
K [auth B],
M [auth C],
P [auth D],
S [auth E],
U [auth F],
W [auth G],
Z [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
BA [auth H],
O [auth C],
R [auth D],
Y [auth G]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth H],
N [auth C],
Q [auth D],
X [auth G]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.856α = 90
b = 94.403β = 102.3
c = 145.124γ = 90
Software Package:
Software NamePurpose
ADSCdata 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
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description