5MUY

Structure of a C-terminal domain of a reptarenavirus L protein with m7GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.0 of the entry. See complete history


Literature

Structural insights into reptarenavirus cap-snatching machinery.

Rosenthal, M.Gogrefe, N.Vogel, D.Reguera, J.Rauschenberger, B.Cusack, S.Gunther, S.Reindl, S.

(2017) PLoS Pathog 13: e1006400-e1006400

  • DOI: https://doi.org/10.1371/journal.ppat.1006400
  • Primary Citation of Related Structures:  
    5MUS, 5MUY, 5MUZ, 5MV0

  • PubMed Abstract: 

    Cap-snatching was first discovered in influenza virus. Structures of the involved domains of the influenza virus polymerase, namely the endonuclease in the PA subunit and the cap-binding domain in the PB2 subunit, have been solved. Cap-snatching endonucleases have also been demonstrated at the very N-terminus of the L proteins of mammarena-, orthobunya-, and hantaviruses. However, a cap-binding domain has not been identified in an arena- or bunyavirus L protein so far. We solved the structure of the 326 C-terminal residues of the L protein of California Academy of Sciences virus (CASV), a reptarenavirus, by X-ray crystallography. The individual domains of this 37-kDa fragment (L-Cterm) as well as the domain arrangement are structurally similar to the cap-binding and adjacent domains of influenza virus polymerase PB2 subunit, despite the absence of sequence homology, suggesting a common evolutionary origin. This enabled identification of a region in CASV L-Cterm with similarity to a cap-binding site; however, the typical sandwich of two aromatic residues was missing. Consistent with this, cap-binding to CASV L-Cterm could not be detected biochemically. In addition, we solved the crystal structure of the corresponding endonuclease in the N-terminus of CASV L protein. It shows a typical endonuclease fold with an active site configuration that is essentially identical to that of known mammarenavirus endonuclease structures. In conclusion, we provide evidence for a presumably functional cap-snatching endonuclease in the N-terminus and a degenerate cap-binding domain in the C-terminus of a reptarenavirus L protein. Implications of these findings for the cap-snatching mechanism in arenaviruses are discussed.


  • Organizational Affiliation

    Department of Virology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L protein
A, B
328CAS virusMutation(s): 0 
EC: 2.7.7.48
UniProt
Find proteins for J7HBG8 (CAS virus)
Explore J7HBG8 
Go to UniProtKB:  J7HBG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ7HBG8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGT
Query on MGT

Download Ideal Coordinates CCD File 
C [auth B]7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE
C11 H20 N5 O14 P3
BUJQMJUTTBGELS-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.34α = 90
b = 76.601β = 90
c = 116.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGTClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyRE 3712/1-1
German Research FoundationGermanyGU 883/1-1
German Research FoundationGermanyGU 883/4-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Database references
  • Version 2.0: 2024-01-17
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Refinement description