3SIS | pdb_00003sis

Crystal structure of Porcine CRW-8 Rotavirus VP8* in complex with aceramido-GM3_Gc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history

Literature

Novel structural insights into rotavirus recognition of ganglioside glycan receptors.

Yu, X.Coulson, B.S.Fleming, F.E.Dyason, J.C.von Itzstein, M.Blanchard, H.

(2011) J Mol Biology 413: 929-939

  • DOI: https://doi.org/10.1016/j.jmb.2011.09.005
  • Primary Citation Related Structures: 
    3SIS, 3SIT

  • PubMed Abstract: 

    Rotaviruses ubiquitously infect children under the age of 5, being responsible for more than half a million diarrhoeal deaths each year worldwide. Host cell oligosaccharides containing sialic acid(s) are critical for attachment by rotaviruses. However, to date, no detailed three-dimensional atomic model showing the exact rotavirus interactions with these glycoconjugate receptors has been reported. Here, we present the first crystallographic structures of the rotavirus carbohydrate-recognizing protein VP8* in complex with ganglioside G(M3) glycans. In combination with assessment of the inhibition of rotavirus infectivity by N-acetyl and N-glycolyl forms of this ganglioside, our results reveal key details of rotavirus-ganglioside G(M3) glycan recognition. In addition, they show a direct correlation between the carbohydrate specificities exhibited by VP8* from porcine and by monkey rotaviruses and the respective infectious virus particles. These novel results also indicate the potential binding interactions of rotavirus VP8* with other sialic acid-containing gangliosides.


  • Organizational Affiliation
    • Institute for Glycomics, Gold Coast campus, Griffith University, Queensland 4222, Australia.

Macromolecule Content 

  • Total Structure Weight: 38.07 kDa 
  • Atom Count: 2,814 
  • Modeled Residue Count: 322 
  • Deposited Residue Count: 326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B
163Porcine rotavirus (serotype 3 / strain CRW-8)Mutation(s): 4 
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
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan: G50281RU
GlyCosmos: G50281RU
GlyGen: G50281RU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.238 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.31α = 90
b = 56.77β = 90
c = 110.7γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Database references
  • Version 1.2: 2011-11-30
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary