4YG6 | pdb_00004yg6

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 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4YG6

This is version 2.1 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: https://doi.org/10.1038/ncomms9346
  • Primary Citation Related Structures: 
    4YFW, 4YFZ, 4YG0, 4YG3, 4YG6

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 75.14 kDa 
  • Atom Count: 6,759 
  • Modeled Residue Count: 651 
  • Deposited Residue Count: 652 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid protein VP8*
A, B, C, D
163Rotavirus A RVA/Cow-tc/USA/B223/1983/G10P[11]Mutation(s): 0 
UniProt
Find proteins for A2T3T2 (Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2]))
Explore A2T3T2 
Go to UniProtKB:  A2T3T2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2T3T2
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
E, F, G
4N/A
Glycosylation Resources
GlyTouCan: G58896AZ
GlyCosmos: G58896AZ
GlyGen: G58896AZ
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
2N/A
Glycosylation Resources
GlyTouCan: G00055MO
GlyCosmos: G00055MO
GlyGen: G00055MO

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free:  0.197 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.2α = 90
b = 140.28β = 90.78
c = 54.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI36040

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary