7KI5

Crystal structure of P[6] rotavirus vp8* in complex with LNT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.

Xu, S.McGinnis, K.R.Liu, Y.Huang, P.Tan, M.Stuckert, M.R.Burnside, R.E.Jacob, E.G.Ni, S.Jiang, X.Kennedy, M.A.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2107963118
  • Primary Citation of Related Structures:  
    6UT9, 6VKX, 7JHZ, 7KHU, 7KI5

  • PubMed Abstract: 

    Group A rotaviruses cause severe gastroenteritis in infants and young children worldwide, with P[II] genogroup rotaviruses (RVs) responsible for >90% of global cases. RVs have diverse host ranges in different human and animal populations determined by host histo-blood group antigen (HBGA) receptor polymorphism, but details governing diversity, host ranges, and species barriers remain elusive. In this study, crystal structures of complexes of the major P[II] genogroup P[4] and P[8] genotype RV VP8* receptor-binding domains together with Lewis epitope-containing LNDFH I glycans in combination with VP8* receptor-glycan ligand affinity measurements based on NMR titration experiments revealed the structural basis for RV genotype-specific switching between ββ and βα HBGA receptor-binding sites that determine RV host ranges. The data support the hypothesis that P[II] RV evolution progressed from animals to humans under the selection of type 1 HBGAs guided by stepwise host synthesis of type 1 ABH and Lewis HBGAs. The results help explain disease burden, species barriers, epidemiology, and limited efficacy of current RV vaccines in developing countries. The structural data has the potential to impact the design of future vaccine strategies against RV gastroenteritis.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D
160Human rotavirus AMutation(s): 0 
Gene Names: VP4
UniProt
Find proteins for Q91E88 (Human rotavirus A)
Explore Q91E88 
Go to UniProtKB:  Q91E88
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91E88
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
E
4N/A
Glycosylation Resources
GlyTouCan:  G00049MO
GlyCosmos:  G00049MO
GlyGen:  G00049MO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.681α = 90
b = 75.354β = 91.77
c = 74.411γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
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: 2021-08-18
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description