7C8P

Structural and functional characterization of human group A rotavirus P[25] VP8*


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen.

Li, D.Wang, M.Qi, J.Zhang, Q.Wang, H.Pang, L.Sun, X.Duan, Z.

(2021) Virology 555: 56-63

  • DOI: https://doi.org/10.1016/j.virol.2020.12.016
  • Primary Citation of Related Structures:  
    7C8P

  • PubMed Abstract: 

    Rotavirus (RV) is a common cause of acute gastroenteritis in young children. While P[8] and P[4] are the most prevalent RV genotypes in humans, other genotypes are also reported in human infections occasionally, including human P[25]. The glycan binding and structural characteristics of human P[25] were explored in our study. Human P[25] VP8* recognized type A histo-blood group antigen (HBGA) in the glycan microarray/oligosaccharide binding assay and could specifically hemagglutinate type A blood cells. Moreover, the P[25] VP8* structure was determined at 2.6 Å, revealing a similar conformation and a conserved putative glycan binding site as that of P[14] VP8*. This study provided further knowledge of the glycan binding and structural features of P[25] RV VP8*, promoting our understanding of the infection, prevalence, and host range of the P[III] RVs.


  • Organizational Affiliation

    National Health Commission Key Laboratory for Medical Virology and Viral Diseases, Beijing, 102206, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, 102206, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B
161Rotavirus AMutation(s): 0 
UniProt
Find proteins for M1GR78 (Rotavirus A)
Explore M1GR78 
Go to UniProtKB:  M1GR78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM1GR78
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.419α = 90
b = 164.419β = 90
c = 164.419γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China2018ZX10711-001
National Natural Science Foundation of China (NSFC)China21934005

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description