8PAG

Crystal structure of the ectodomain of Norway rat pestivirus E2 glycoprotein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural comparison of typical and atypical E2 pestivirus glycoproteins.

Aitkenhead, H.Riedel, C.Cowieson, N.Rumenapf, H.T.Stuart, D.I.El Omari, K.

(2024) Structure 32: 273-281.e4

  • DOI: https://doi.org/10.1016/j.str.2023.12.003
  • Primary Citation of Related Structures:  
    8PAB, 8PAE, 8PAG

  • PubMed Abstract: 

    Pestiviruses, within the family Flaviviridae, are economically important viruses of livestock. In recent years, new pestiviruses have been reported in domestic animals and non-cloven-hoofed animals. Among them, atypical porcine pestivirus (APPV) and Norway rat pestivirus (NRPV) have relatively little sequence conservation in their surface glycoprotein E2. Despite E2 being the main target for neutralizing antibodies and necessary for cell attachment and viral fusion, the mechanism of viral entry remains elusive. To gain further insights into the pestivirus E2 mechanism of action and to assess its diversity within the genus, we report X-ray structures of the pestivirus E2 proteins from APPV and NRPV. Despite the highly divergent structures, both are able to dimerize through their C-terminal domain and contain a solvent-exposed β-hairpin reported to be involved in host receptor binding. Functional analysis of this β-hairpin in the context of BVDV revealed its ability to rescue viral infectivity.


  • Organizational Affiliation

    Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxfordshire OX11 0FA, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, Oxfordshire OX3 7BN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Genome polyprotein381Norway rat pestivirusMutation(s): 0 
UniProt
Find proteins for A0A097NZ77 (Pestivirus ratti)
Explore A0A097NZ77 
Go to UniProtKB:  A0A097NZ77
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A097NZ77
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC
GlyCosmos:  G22573RC
GlyGen:  G22573RC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.270 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.92α = 90
b = 151.92β = 90
c = 59.88γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M011224/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release