5KW9

Structural Basis for Norovirus Neutralization by a HBGA Blocking Human IgA Antibody

  • Classification: ANTIVIRAL PROTEIN
  • Organism(s): Norwalk virus, Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2016-07-15 Released: 2016-10-05 
  • Deposition Author(s): Shanker, S., Prasad, B.V.V.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for norovirus neutralization by an HBGA blocking human IgA antibody.

Shanker, S.Czako, R.Sapparapu, G.Alvarado, G.Viskovska, M.Sankaran, B.Atmar, R.L.Crowe, J.E.Estes, M.K.Prasad, B.V.

(2016) Proc Natl Acad Sci U S A 113: E5830-E5837

  • DOI: 10.1073/pnas.1609990113
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Human noroviruses (HuNoVs) cause sporadic and epidemic gastroenteritis worldwide. They are classified into two major genogroups (GI and GII), with each genogroup further divided into multiple genotypes. Susceptibility to these viruses is influenced b ...

    Human noroviruses (HuNoVs) cause sporadic and epidemic gastroenteritis worldwide. They are classified into two major genogroups (GI and GII), with each genogroup further divided into multiple genotypes. Susceptibility to these viruses is influenced by genetically determined histo-blood group antigen (HBGA) expression. HBGAs function as cell attachment factors by binding to a surface-exposed region in the protruding (P) domain of the capsid protein. Sequence variations in this region that result in differential HBGA binding patterns and antigenicity are suggested to form a basis for strain diversification. Recent studies show that serum antibodies that block HBGA binding correlate with protection against illness. Although genogroup-dependent variation in HBGA binding specificity is structurally well characterized, an understanding of how antibodies block HBGA binding and how genotypic variations affect such blockade is lacking. Our crystallographic studies of the GI.1 P domain in complex with the Fab fragment of a human IgA monoclonal antibody (IgA 5I2) with HBGA blocking activity show that the antibody recognizes a conformational epitope formed by two surface-exposed loop clusters in the P domain. The antibody engulfs the HBGA binding site but does not affect its structural integrity. An unusual feature of the antigen recognition by IgA 5I2 is the predominant involvement of the CDR light chain 1 in contrast to the commonly observed CDR heavy chain 3, providing a unique perspective into antibody diversity in antigen recognition. Identification of the antigenic site in the P domain shows how genotypic variations might allow escape from antibody neutralization and exemplifies the interplay between antigenicity and HBGA specificity in HuNoV evolution.


    Organizational Affiliation

    The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; mestes@bcm.edu vprasad@bcm.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A
295Norwalk virusMutation(s): 0 
Find proteins for Q83884 (Norwalk virus (strain GI/Human/United States/Norwalk/1968))
Go to UniProtKB:  Q83884

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IgA(VH)-IgG(CH) heavy chain Fab fragment
H
227Homo sapiensMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
IgA Light chain
L
220Homo sapiensMutation(s): 0 
Membrane protein
inferred by homology
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
M2 human muscarinic acetylcholine receptor-β-arrestin complex in a nanodisc
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
A, H, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162α = 90
b = 162β = 90
c = 146.81γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI057788
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesP30 DK56338

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Structure summary
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence