3ZL9

Crystal structure of the nucleocapsid protein from Schmallenberg virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Nucleocapsid Protein Structures from Orthobunyaviruses Reveal Insight Into Ribonucleoprotein Architecture and RNA Polymerization.

Ariza, A.Tanner, S.J.Walter, C.T.Dent, K.C.Shepherd, D.A.Wu, W.Matthews, S.V.Hiscox, J.A.Green, T.J.Luo, M.Elliott, R.M.Fooks, A.R.Ashcroft, A.E.Stonehouse, N.J.Ranson, N.A.Barr, J.N.Edwards, T.A.

(2013) Nucleic Acids Res 41: 5912

  • DOI: 10.1093/nar/gkt268
  • Primary Citation of Related Structures:  
    3ZLA, 3ZL9

  • PubMed Abstract: 
  • All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N-RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3 ...

    All orthobunyaviruses possess three genome segments of single-stranded negative sense RNA that are encapsidated with the virus-encoded nucleocapsid (N) protein to form a ribonucleoprotein (RNP) complex, which is uncharacterized at high resolution. We report the crystal structure of both the Bunyamwera virus (BUNV) N-RNA complex and the unbound Schmallenberg virus (SBV) N protein, at resolutions of 3.20 and 2.75 Å, respectively. Both N proteins crystallized as ring-like tetramers and exhibit a high degree of structural similarity despite classification into different orthobunyavirus serogroups. The structures represent a new RNA-binding protein fold. BUNV N possesses a positively charged groove into which RNA is deeply sequestered, with the bases facing away from the solvent. This location is highly inaccessible, implying that RNA polymerization and other critical base pairing events in the virus life cycle require RNP disassembly. Mutational analysis of N protein supports a correlation between structure and function. Comparison between these crystal structures and electron microscopy images of both soluble tetramers and authentic RNPs suggests the N protein does not bind RNA as a repeating monomer; thus, it represents a newly described architecture for bunyavirus RNP assembly, with implications for many other segmented negative-strand RNA viruses.


    Organizational Affiliation

    School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NUCLEOCAPSID PROTEINA, B, C, D234Schmallenberg virusMutation(s): 0 
UniProt
Find proteins for H2AM13 (Bovine Schmallenberg virus (isolate Bovine/BH80/Germany/2011))
Explore H2AM13 
Go to UniProtKB:  H2AM13
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.03α = 90
b = 81.03β = 90
c = 128.551γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references