3ZL9 | pdb_00003zl9

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 (Depositor) 
  • R-Value Work: 
    0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 3ZL9

This is version 1.2 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: https://doi.org/10.1093/nar/gkt268
  • Primary Citation Related Structures: 
    3ZL9, 3ZLA

  • 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 3.20 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.

Macromolecule Content 

  • Total Structure Weight: 105.18 kDa 
  • Atom Count: 7,182 
  • Modeled Residue Count: 903 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NUCLEOCAPSID PROTEIN
A, B, C, D
234Schmallenberg virusMutation(s): 0 
UniProt
Find proteins for H2AM13 (Bovine Schmallenberg virus (isolate Bovine/BH80/Germany/2011))
Explore H2AM13 
Go to UniProtKB:  H2AM13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2AM13
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.201 (Depositor) 
  • R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
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

View Full Validation Report



Entry History 

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
  • Version 1.2: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description