4H5P

Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Tetramer Bound to Single-stranded RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Phleboviruses encapsidate their genomes by sequestering RNA bases.

Raymond, D.D.Piper, M.E.Gerrard, S.R.Skiniotis, G.Smith, J.L.

(2012) Proc Natl Acad Sci U S A 109: 19208-19213

  • DOI: https://doi.org/10.1073/pnas.1213553109
  • Primary Citation of Related Structures:  
    4H5L, 4H5M, 4H5O, 4H5P, 4H5Q, 4V9E

  • PubMed Abstract: 

    Rift Valley fever and Toscana viruses are human pathogens for which no effective therapeutics exist. These and other phleboviruses have segmented negative-sense RNA genomes that are sequestered by a nucleocapsid protein (N) to form ribonucleoprotein (RNP) complexes of irregular, asymmetric structure, previously uncharacterized at high resolution. N binds nonspecifically to single-stranded RNA with nanomolar affinity. Crystal structures of Rift Valley fever virus N-RNA complexes reconstituted with defined RNAs of different length capture tetrameric, pentameric and hexameric N-RNA multimers. All N-N subunit contacts are mediated by a highly flexible α-helical arm. Arm movement gives rise to the three multimers in the crystal structures and also explains the asymmetric architecture of the RNP. Despite the flexible association of subunits, the crystal structures reveal an invariant, monomeric RNP building block, consisting of the core of one N subunit, the arm of a neighboring N, and four RNA nucleotides with the flanking phosphates. Up to three additional RNA nucleotides bind between subunits. The monomeric building block is matched in size to the repeating unit in viral RNP, as visualized by electron microscopy. N sequesters four RNA bases in a narrow hydrophobic binding slot and has polar contacts only with the sugar-phosphate backbone, which faces the solvent. All RNA bases, whether in the binding slot or in the subunit interface, face the protein in a manner that is incompatible with base pairing or with "reading" by the viral polymerase.


  • Organizational Affiliation

    Life Sciences Institute, Department of Biological Chemistry, Cell and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleocapsid protein
A, B, C, D
245Rift Valley fever virusMutation(s): 0 
Gene Names: N
UniProt
Find proteins for D3K5I7 (Rift valley fever virus)
Explore D3K5I7 
Go to UniProtKB:  D3K5I7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3K5I7
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
28-mer poly(U) RNA
E, F
14N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.64α = 90
b = 193.18β = 108.89
c = 77.42γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHASERphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-21
    Changes: Database references
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Refinement description