4YG6

Structural basis of glycan recognition in neonate-specific rotaviruses


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus.

Hu, L.Ramani, S.Czako, R.Sankaran, B.Yu, Y.Smith, D.F.Cummings, R.D.Estes, M.K.Venkataram Prasad, B.V.

(2015) Nat Commun 6: 8346-8346

  • DOI: 10.1038/ncomms9346
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and chil ...

    Strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type II precursor glycans, and to restrict type II glycan binding in the bovine counterpart. Such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.


    Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer capsid protein VP8*
A, B, C, D
163Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2])Mutation(s): 0 
Find proteins for A2T3T2 (Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2]))
Go to UniProtKB:  A2T3T2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B, C
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B, C, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.200α = 90.00
b = 140.280β = 90.78
c = 54.600γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-02-25 
  • Released Date: 2015-09-30 
  • Deposition Author(s): Hu, L., Prasad, B.V.V.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI36040

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Advisory, Author supporting evidence, Derived calculations