6JYS | pdb_00006jys

GII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6JYS

This is version 2.2 of the entry. See complete history

Literature

GII.13/21 Noroviruses Recognize Glycans with a Terminal beta-Galactose via an Unconventional Glycan Binding Site.

Cong, X.Sun, X.M.Qi, J.X.Li, H.B.Chai, W.G.Zhang, Q.Wang, H.Kong, X.Y.Song, J.Pang, L.L.Jin, M.Li, D.D.Tan, M.Duan, Z.J.

(2019) J Virol 93

  • DOI: https://doi.org/10.1128/JVI.00723-19
  • Primary Citation Related Structures: 
    6JYN, 6JYO, 6JYR, 6JYS

  • PubMed Abstract: 

    Human noroviruses (huNoVs) recognize histo-blood group antigens (HBGAs) as host susceptibility factors. GII.13 and GII.21 huNoVs form a unique genetic lineage that emerged from mainstream GII NoVs via development of a new, nonconventional glycan binding site (GBS) that binds Le a antigen. This previous finding raised the question of whether the new GII.13/21 GBS really has such a narrow glycan binding spectrum. In this study, we provide solid phenotypic and structural evidence indicating that this new GBS recognizes a group of glycans with a common terminal β-galactose (β-Gal). First, we found that P domain proteins of GII.13/21 huNoVs circulating at different times bound three glycans sharing a common terminal β-Gal, including Lec, lactose, and mucin core 2. Second, we solved the crystal structures of the GII.13 P dimers in complex with Lec and mucin core 2, which showed that β-Gal is the major binding saccharide. Third, nonfat milk and lactose blocked the GII.13/21 P domain-glycan binding, which may explain the low prevalence of GII.13/21 viruses. Our data provide new insight into the host interactions and epidemiology of huNoVs, which would help in the control and prevention of NoV-associated diseases. IMPORTANCE Evidence from both phenotypic binding assay and structural study support the observed interactions of human noroviruses (huNoVs) with histo-blood group antigens (HBGAs) as receptors or attachment factors, affecting their host susceptibility. GII.13 and GII.21 genotypes form a unique genetic lineage that differs from the mainstream GII huNoVs in their unconventional glycan binding site. Unlike the previous findings that GII.13/21 genotypes recognize only Le a antigen, we found in this study that they can interact with a group of glycans with a common terminal β-Gal, including Lec, lactose, and mucin core 2. However, this wide glycan binding spectrum in a unique binding mode of the GII.13/21 huNoVs appears not to increase their prevalence, probably due to the existence of decoy glycan receptors in human gastrointestinal tract limiting their infection. Our findings shed light on the host interaction and epidemiology of huNoVs, which would impact the strategy of huNoV control and prevention.


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

Macromolecule Content 

  • Total Structure Weight: 137.48 kDa 
  • Atom Count: 11,371 
  • Modeled Residue Count: 1,232 
  • Deposited Residue Count: 1,232 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
human norovirus P protein
A, B, C, D
308Alphatron virusMutation(s): 0 
UniProt
Find proteins for A0A509GV48 (Alphatron virus)
Explore A0A509GV48 
Go to UniProtKB:  A0A509GV48
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A509GV48
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-alpha-D-galactopyranose
E, G, H
2N/A
Glycosylation Resources
GlyTouCan: G00031MO
GlyCosmos: G00031MO
GlyGen: G00031MO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose
F
3N/A
Glycosylation Resources
GlyTouCan: G00033MO
GlyCosmos: G00033MO
GlyGen: G00033MO

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THR

Query on THR



Download:Ideal Coordinates CCD File
I [auth B]THREONINE
C4 H9 N O3
AYFVYJQAPQTCCC-GBXIJSLDSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.728α = 90
b = 99.695β = 90
c = 221.824γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)Chinano.2018ZA10711-001 and no.2017ZX10104001

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-31
    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: 2024-03-06
    Changes: Data collection, Database references, Structure summary
  • Version 2.2: 2024-05-01
    Changes: Derived calculations