3JSB | pdb_00003jsb

Crystal structure of the N-terminal domain of the Lymphocytic Choriomeningitis Virus L protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

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This is version 1.3 of the entry. See complete history

Literature

The N-terminal domain of the arenavirus L protein is an RNA endonuclease essential in mRNA transcription

Morin, B.Coutard, B.Lelke, M.Ferron, F.P.Kerber, R.Jamal, S.Frangeul, A.Baronti, C.Charrel, R.de Lamballerie, X.Vonrhein, C.Lescar, J.Bricogne, G.Gunther, S.Canard, B.

(2010) PLoS Pathog 6: e1001038-e1001038

  • DOI: https://doi.org/10.1371/journal.ppat.1001038
  • Primary Citation Related Structures: 
    3JSB

  • PubMed Abstract: 

    Arenaviridae synthesize viral mRNAs using short capped primers presumably acquired from cellular transcripts by a 'cap-snatching' mechanism. Here, we report the crystal structure and functional characterization of the N-terminal 196 residues (NL1) of the L protein from the prototypic arenavirus: lymphocytic choriomeningitis virus. The NL1 domain is able to bind and cleave RNA. The 2.13 Å resolution crystal structure of NL1 reveals a type II endonuclease α/β architecture similar to the N-terminal end of the influenza virus PA protein. Superimposition of both structures, mutagenesis and reverse genetics studies reveal a unique spatial arrangement of key active site residues related to the PD…(D/E)XK type II endonuclease signature sequence. We show that this endonuclease domain is conserved and active across the virus families Arenaviridae, Bunyaviridae and Orthomyxoviridae and propose that the arenavirus NL1 domain is the Arenaviridae cap-snatching endonuclease.


  • Organizational Affiliation
    • Architecture et Fonction des Macromolécules Biologiques, CNRS and Universités d'Aix-Marseille I et II, UMR 6098, ESIL Case 925, Marseille, France.

Macromolecule Content 

  • Total Structure Weight: 47.44 kDa 
  • Atom Count: 3,259 
  • Modeled Residue Count: 367 
  • Deposited Residue Count: 408 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA-directed RNA polymerase
A, B
204Lymphocytic choriomeningitis virus (strain Armstrong)Mutation(s): 2 
Gene Names: L
EC: 2.7.7.48 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P14240 (Lymphocytic choriomeningitis virus (strain Armstrong))
Explore P14240 
Go to UniProtKB:  P14240
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14240
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.01α = 90
b = 159.35β = 90
c = 52.62γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-15
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references