6E47

Crystal Structure of the Murine Norovirus VP1 P domain in complex with the CD300lf Receptor and Glycochenodeoxycholic Acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor.

Wilen, C.B.Dai, Y.N.Orchard, R.C.Kim, A.S.Stegeman, R.A.Hsieh, L.L.Smith, T.J.Virgin, H.W.Fremont, D.H.Nelson, C.A.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E9201-E9210

  • DOI: 10.1073/pnas.1805797115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its ce ...

    Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor.


    Organizational Affiliation

    Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; svirgin@vir.bio fremont@wustl.edu.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1 P domain
A, B
302Murine norovirus 1Mutation(s): 0 
Find proteins for Q80J94 (Murine norovirus 1)
Go to UniProtKB:  Q80J94
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CMRF35-like molecule 1
F, G
112Mus musculusMutation(s): 0 
Gene Names: Cd300lf (Clm1, Lmir3)
Find proteins for Q6SJQ7 (Mus musculus)
Go to UniProtKB:  Q6SJQ7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHO
Query on CHO

Download SDF File 
Download CCD File 
B
GLYCOCHENODEOXYCHOLIC ACID
C26 H43 N O5
GHCZAUBVMUEKKP-GYPHWSFCSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, F, G
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.105α = 90.00
b = 134.824β = 90.00
c = 139.592γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI109725
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI127552

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence