2I2S

Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: in silico
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This is version 1.5 of the entry. See complete history


Literature

Insight into Host Cell Carbohydrate-recognition by Human and Porcine Rotavirus from Crystal Structures of the Virion Spike Associated Carbohydrate-binding Domain (VP8*)

Blanchard, H.Yu, X.Coulson, B.S.von Itzstein, M.

(2007) J Mol Biol 367: 1215-1226

  • DOI: https://doi.org/10.1016/j.jmb.2007.01.028
  • Primary Citation of Related Structures:  
    2DWR, 2I2S

  • PubMed Abstract: 

    Rotavirus infection leads to the death of half a million children annually. The exact specifics of interaction between rotavirus particles and host cells enabling invasion and infection have remained elusive. Host cell oligosaccharides are critical components, and their involvement aids the virus in cell-recognition and attachment, as well as dictation of the remarkable host-specificity that rotaviruses demonstrate. Interaction between the rotavirus spike-protein carbohydrate-binding domain (VP8*) and cell surface oligosaccharides facilitate virus recognition of host cells and attachment. Rotaviruses are considered, controversially, to recognise vastly different carbohydrate structures and either with incorporation of terminal sialic acid or without, as assessed by their ability to infect cells that have been pre-treated with sialidases. Herein, the X-ray crystallographic structures of VP8* from the sialidase insensitive Wa and the sialidase sensitive CRW-8 rotavirus strains that cause debilitating gastroenteritis in human and pig are reported. Striking differences are apparent regarding recognition of the sialic acid derivative methyl alpha-D-N-acetylneuraminide, presenting the first experimental evidence of the inability of the human rotavirus strain to bind this monosaccharide, that correlates with Wa and CRW-8 recognising sialidase-resistant and sialidase-sensitive receptors, respectively. Identified are structural features that provide insight in attainment of substrate specificity exhibited by porcine strains as compared to rhesus rotavirus. Revealed in the CRW-8 VP8* structure is an additional bound ligand that intriguingly, is within a cleft located equivalent to the carbohydrate-binding region of galectins, and is suggestive of a new region for interaction with cell-surface carbohydrates. This novel result and detailed comparison of our representative sialidase-sensitive CRW-8 and insensitive Wa VP8* structures with those reported leads to our hypothesis that this groove is used for binding carbohydrates, and that for the human strains, as for other sialidase-insensitive strains could represent a major oligosaccharide-binding region.


  • Organizational Affiliation

    Institute for Glycomics, Griffith University, Gold Coast Campus, PMB 50 Gold Coast Mail Centre, Queensland, 9726, Australia. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B
163Porcine rotavirusMutation(s): 0 
UniProt
Find proteins for P0C6Y8 (Rotavirus A (isolate RVA/Pig/Australia/CRW-8/1987/G3P9[7]))
Explore P0C6Y8 
Go to UniProtKB:  P0C6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6Y8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MNA
Query on MNA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B]
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid
C12 H21 N O9
NJRVVFURCKKXOD-MIDKXNQYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.929α = 90
b = 64.663β = 90
c = 109.886γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XNEWMOdata collection
FIPdata collection
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2024-04-03
    Changes: Refinement description