9EN4 | pdb_00009en4

VP8* domain of the spike protein VP4 from bovine P[3] strain of rotavirus species C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.297 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interaction of the VP8* protein of a bovine rotavirus C with the H type-2 antigen and its precursor N-acetyl-lactosamine.

Navarro-Lleo, N.Ramirez-Cardenas, J.Paredes-Martinez, F.Serna, S.Gozalbo-Rovira, R.Munoz-Garcia, J.C.Reichardt, N.C.Casino, P.Angulo, J.Rodriguez-Diaz, J.Buesa, J.

(2025) Int J Biol Macromol : 149621-149621

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.149621
  • Primary Citation of Related Structures:  
    9EN4

  • PubMed Abstract: 

    Rotaviruses (RVs) are the main cause of viral diarrhea among infants, small children, and the young of many animal species. Histo-blood group antigens (HBGAs) are potential RV receptors and glycan composition on mucous surfaces influences host susceptibility and cross-species virus transmission. RVs exhibit genotype-dependent glycan binding and differences are due to sequence modifications in the VP8* domain of the spike protein VP4. Nevertheless, the molecular bases for this genotype-dependent glycan specificity, especially in non-A RVs, are not thoroughly understood. This study delves into how genotypic variations configure a novel binding site in the VP8* of a bovine P[3] rotavirus species C (RVC) strain to recognize H type-2 antigen (H2) and its precursor N-acetyl-lactosamine (LacNAc) using glycan binding assays, crystallography, and STD NMR. Results reveal a specific interaction of bovine P[3] RVC VP8* with H2 and LacNAc, more strongly with the latter. In the P[3] RVC VP8*-H2 interaction, the N-acetyl glucosamine moiety displays significant interaction, while galactose participates moderately and fucose binds weakly. Moreover, the bovine VP8* structure, resolved at 3 Å, shows specific structural features which differ from human RVC, as it contains two additional β-strands (β1 and β2) contributing to β-sheet2 and conformational changes that widens the cleft to allow different carbohydrate binding modes. These subtle changes in both sequence and structure explain the H2 precursor recognition, which is abundant in the human neonate intestine and in human and bovine milk, providing insights into P[3] RVC tropism and its potential zoonotic transmission.


  • Organizational Affiliation
    • Departament de Microbiologia, Facultat de Medicina i Odontologia, Universitat de València, 46010, Valencia, Spain. Electronic address: noemi.navarro@uv.es.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer capsid protein VP8*
A, B
165Bovine rotavirus CMutation(s): 0 
Gene Names: VP4
UniProt
Find proteins for Q65525 (Rotavirus C (isolate RVC/Cow/Japan/Shintoku/1991/G2P[3]))
Explore Q65525 
Go to UniProtKB:  Q65525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ65525
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.297 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.489α = 90
b = 64.37β = 90
c = 76.937γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2019- 110630 GB-I00
European Regional Development FundEuropean UnionPID2022-141621NB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Structure summary
  • Version 1.2: 2025-12-24
    Changes: Database references