5YMT | pdb_00005ymt

Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

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

Literature

Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s.

Sun, X.Li, D.Qi, J.Chai, W.Wang, L.Wang, L.Peng, R.Wang, H.Zhang, Q.Pang, L.Kong, X.Wang, H.Jin, M.Gao, G.F.Duan, Z.

(2018) J Virol 92

  • DOI: https://doi.org/10.1128/JVI.00538-18
  • Primary Citation Related Structures: 
    5YMS, 5YMT, 5YMU

  • PubMed Abstract: 

    Rotaviruses (RVs), which cause severe gastroenteritis in infants and children, recognize glycan ligands in a genotype-dependent manner via the distal VP8* head of the spike protein VP4. However, the glycan binding mechanisms remain elusive for the P[II] genogroup RVs, including the widely prevalent human RVs (P[8], P[4], and P[6]) and a rare P[19] RV. In this study, we characterized the glycan binding specificities of human and porcine P[6]/P[19] RV VP8*s and found that the P[II] genogroup RV VP8*s could commonly interact with mucin core 2, which may play an important role in RV evolution and cross-species transmission. We determined the first P[6] VP8* structure, as well as the complex structures of human P[19] VP8*, with core 2 and lacto- N -tetraose (LNT). A glycan binding site was identified in human P[19] VP8*. Structural superimposition and sequence alignment revealed the conservation of the glycan binding site in the P[II] genogroup RV VP8*s. Our data provide significant insight into the glycan binding specificity and glycan binding mechanism of the P[II] genogroup RV VP8*s, which could help in understanding RV evolution, transmission, and epidemiology and in vaccine development. IMPORTANCE Rotaviruses (RVs), belonging to the family Reoviridae , are double-stranded RNA viruses that cause acute gastroenteritis in children and animals worldwide. Depending on the phylogeny of the VP8* sequences, P[6] and P[19] RVs are grouped into genogroup II, together with P[4] and P[8], which are widely prevalent in humans. In this study, we characterized the glycan binding specificities of human and porcine P[6]/P[19] RV VP8*s, determined the crystal structure of P[6] VP8*, and uncovered the glycan binding pattern in P[19] VP8*, revealing a conserved glycan binding site in the VP8*s of P[II] genogroup RVs by structural superimposition and sequence alignment. Our data suggested that mucin core 2 may play an important role in P[II] RV evolution and cross-species transmission. These data provide insight into the cell attachment, infection, epidemiology, and evolution of P[II] genogroup RVs, which could help in developing control and prevention strategies against RVs.


  • Organizational Affiliation
    • Key Laboratory of Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 255.83 kDa 
  • Atom Count: 18,722 
  • Modeled Residue Count: 2,240 
  • Deposited Residue Count: 2,240 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Outer capsid protein VP4
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
160Human rotavirus AMutation(s): 0 
UniProt
Find proteins for Q9Q2P6 (Human rotavirus A)
Explore Q9Q2P6 
Go to UniProtKB:  Q9Q2P6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Q2P6
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
O, P, Q
4N/A
Glycosylation Resources
GlyTouCan: G19979XJ
GlyCosmos: G19979XJ
GlyGen: G19979XJ

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.667α = 90
b = 131.667β = 90
c = 150.53γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81472003; 31500139;81601813

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-05-23
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-11
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary