5CB7

Crystallographic structure of human rotavirus K8 VP8* in complex with A-type HBGA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Substantial Receptor-induced Structural Rearrangement of Rotavirus VP8*: Potential Implications for Cross-Species Infection.

Yu, X.Mishra, R.Holloway, G.von Itzstein, M.Coulson, B.S.Blanchard, H.

(2015) Chembiochem 16: 2176-2181

  • DOI: https://doi.org/10.1002/cbic.201500360
  • Primary Citation of Related Structures:  
    5CA6, 5CAZ, 5CB7

  • PubMed Abstract: 

    Rotavirus-cell binding is the essential first step in rotavirus infection. This binding is a major determinant of rotavirus tropism, as host cell invasion is necessary to initiate infection. Initial rotavirus-cell interactions are mediated by carbohydrate-recognizing domain VP8* of the rotavirus capsid spike protein VP4. Here, we report the first observation of significant structural rearrangement of VP8* from human and animal rotavirus strains upon glycan receptor binding. The structural adaptability of rotavirus VP8* delivers important insights into how human and animal rotaviruses utilize the wider range of cellular glycans identified as VP8* binding partners. Furthermore, our studies on rotaviruses with atypical genetic makeup provide information expected to be critical for understanding the mechanisms of animal rotavirus gene emergence in humans and support implementation of epidemiologic surveillance of animal reservoirs as well as future vaccination schemes.


  • Organizational Affiliation

    Institute for Glycomics, Griffith University Gold Coast Campus, Southport, QLD, 4222, Australia. h.blanchard@griffith.edu.au.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B
161Rotavirus A K8/G1Mutation(s): 1 
UniProt
Find proteins for Q01641 (Rotavirus A (strain RVA/Human/Japan/K8/1977/G1P3A[9]))
Explore Q01641 
Go to UniProtKB:  Q01641
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01641
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose
C, D
3N/A
Glycosylation Resources
GlyTouCan:  G15611BA
GlyCosmos:  G15611BA
GlyGen:  G15611BA
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download Ideal Coordinates CCD File 
E [auth B]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
GAL
Query on GAL

Download Ideal Coordinates CCD File 
F [auth B]beta-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
G [auth B]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
J [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.27α = 90
b = 83.19β = 94.03
c = 47.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1085596

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Structure summary