Leanyer orthobunyavirus nucleoprotein-ssDNA complex

Experimental Data Snapshot

  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

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This is version 1.3 of the entry. See complete history


Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation.

Niu, F.Shaw, N.Wang, Y.E.Jiao, L.Ding, W.Li, X.Zhu, P.Upur, H.Ouyang, S.Cheng, G.Liu, Z.J.

(2013) Proc Natl Acad Sci U S A 110: 9054-9059

  • DOI: https://doi.org/10.1073/pnas.1300035110
  • Primary Citation of Related Structures:  
    4J1G, 4J1J

  • PubMed Abstract: 

    Negative-stranded RNA viruses cover their genome with nucleoprotein (N) to protect it from the human innate immune system. Abrogation of the function of N offers a unique opportunity to combat the spread of the viruses. Here, we describe a unique fold of N from Leanyer virus (LEAV, Orthobunyavirus genus, Bunyaviridae family) in complex with single-stranded RNA refined to 2.78 Å resolution as well as a 2.68 Å resolution structure of LEAV N-ssDNA complex. LEAV N is made up of an N- and a C-terminal lobe, with the RNA binding site located at the junction of these lobes. The LEAV N tetramer binds a 44-nucleotide-long single-stranded RNA chain. Hence, oligomerization of N is essential for encapsidation of the entire genome and is accomplished by using extensions at the N and C terminus. Molecular details of the oligomerization of N are illustrated in the structure where a circular ring-like tertiary assembly of a tetramer of LEAV N is observed tethering the RNA in a positively charged cavity running along the inner edge. Hydrogen bonds between N and the C2 hydroxyl group of ribose sugar explain the specificity of LEAV N for RNA over DNA. In addition, base-specific hydrogen bonds suggest that some regions of RNA bind N more tightly than others. Hinge movements around F20 and V125 assist in the reversal of capsidation during transcription and replication of the virus. Electron microscopic images of the ribonucleoprotein complexes of LEAV N reveal a filamentous assembly similar to those found in phleboviruses.

  • Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NucleocapsidA [auth D],
B [auth A],
C [auth B],
D [auth C]
235Leanyer virusMutation(s): 0 
Find proteins for F2WAD7 (Leanyer virus)
Explore F2WAD7 
Go to UniProtKB:  F2WAD7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF2WAD7
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
F [auth I]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.403α = 70.89
b = 73.199β = 82.54
c = 77.905γ = 73.73
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-12
    Changes: Database references
  • Version 1.2: 2014-11-05
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description