Crystal structure of LC3A in complex with the LIR of NSs4

Experimental Data Snapshot

  • Resolution: 2.24 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 

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An LIR motif in the Rift Valley fever virus NSs protein is critical for the interaction with LC3 family members and inhibition of autophagy.

Petraccione, K.Ali, M.G.H.Cyr, N.Wahba, H.M.Stocker, T.Akhrymuk, M.Akhrymuk, I.Panny, L.Bracci, N.Cafaro, R.Sastre, D.Silberfarb, A.O'Maille, P.Omichinski, J.Kehn-Hall, K.

(2024) PLoS Pathog 20: e1012093-e1012093

  • DOI: https://doi.org/10.1371/journal.ppat.1012093
  • Primary Citation of Related Structures:  
    8T2L, 8T2M, 8T2N

  • PubMed Abstract: 

    Rift Valley fever virus (RVFV) is a viral zoonosis that causes severe disease in ruminants and humans. The nonstructural small (NSs) protein is the primary virulence factor of RVFV that suppresses the host's antiviral innate immune response. Bioinformatic analysis and AlphaFold structural modeling identified four putative LC3-interacting regions (LIR) motifs (NSs 1-4) in the RVFV NSs protein, which suggest that NSs interacts with the host LC3-family proteins. Using, isothermal titration calorimetry, X-ray crystallography, co-immunoprecipitation, and co-localization experiments, the C-terminal LIR motif (NSs4) was confirmed to interact with all six human LC3 proteins. Phenylalanine at position 261 (F261) within NSs4 was found to be critical for the interaction of NSs with LC3, retention of LC3 in the nucleus, as well as the inhibition of autophagy in RVFV infected cells. These results provide mechanistic insights into the ability of RVFV to overcome antiviral autophagy through the interaction of NSs with LC3 proteins.

  • Organizational Affiliation

    Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein S,Microtubule-associated proteins 1A/1B light chain 3A chimera
A, B
132Homo sapiensMutation(s): 0 
Gene Names: NSSMAP1LC3A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H492 (Homo sapiens)
Explore Q9H492 
Go to UniProtKB:  Q9H492
GTEx:  ENSG00000101460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H492
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.24 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.995α = 90
b = 50.267β = 90
c = 137.874γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release