5N7M

Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Human norovirus inhibition by a human milk oligosaccharide.

Koromyslova, A.Tripathi, S.Morozov, V.Schroten, H.Hansman, G.S.

(2017) Virology 508: 81-89

  • DOI: 10.1016/j.virol.2017.04.032
  • Primary Citation of Related Structures:  
    5LKG, 5LKC, 5N7M

  • PubMed Abstract: 
  • Human noroviruses are the leading cause of outbreaks of acute gastroenteritis. Norovirus interactions with histo-blood group antigens (HBGAs) are known to be important for an infection. In this study, we identified the HBGA binding pocket for an emerging GII genotype 17 (GII ...

    Human noroviruses are the leading cause of outbreaks of acute gastroenteritis. Norovirus interactions with histo-blood group antigens (HBGAs) are known to be important for an infection. In this study, we identified the HBGA binding pocket for an emerging GII genotype 17 (GII.17) variant using X-ray crystallography. The GII.17 variant bound the HBGA with an equivalent set of residues as the leading pandemic GII.4 variants. These structural data highlights the conserved nature of HBGA binding site between prevalent GII noroviruses. Noroviruses also interact with human milk oligosaccharides (HMOs), which mimic HBGAs and may function as receptor decoys. We previously showed that HMOs inhibited the binding of rarely detected GII.10 norovirus to HBGAs. We now found that an HMO, 2'-fucosyllactose (2'FL), additionally blocked both the GI.1 and GII.17 noroviruses from binding to HBGAs. Together, these findings provide evidence that 2'FL might function as a broadly reactive antiviral against multiple norovirus genogroups.


    Organizational Affiliation

    Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany. Electronic address: g.hansman@dkfz.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1A, B295Norovirus Hu/1968/USMutation(s): 0 
Gene Names: ORF2
UniProt
Find proteins for Q83884 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Explore Q83884 
Go to UniProtKB:  Q83884
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranoseC, D3 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.07α = 90
b = 84.07β = 90
c = 165.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary