6H9V | pdb_00006h9v

Crystal structure of deaminated P domain from norovirus strain Saga GII-4 in complex with Fuc

• PDB DOI: https://doi.org/10.2210/pdb6H9V/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Hu/GII-4/Saga4/2006/JP
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-06 Released: 2019-04-03 
• Deposition Author(s): Meyer, P.H.O., Blaum, B.S.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 
  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Literature

A post-translational modification of human Norovirus capsid protein attenuates glycan binding.

Mallagaray, A., Creutznacher, R., Dulfer, J., Mayer, P.H.O., Grimm, L.L., Orduna, J.M., Trabjerg, E., Stehle, T., Rand, K.D., Blaum, B.S., Uetrecht, C., Peters, T.

(2019) Nat Commun 10: 1320-1320

• PubMed: 30899001 
• DOI: https://doi.org/10.1038/s41467-019-09251-5
• Primary Citation Related Structures: 
  6H9V


• PubMed Abstract: 
  

  Attachment of human noroviruses to histo blood group antigens (HBGAs) is essential for infection, but how this binding event promotes the infection of host cells is unknown. Here, we employ protein NMR experiments supported by mass spectrometry and crystallography to study HBGA binding to the P-domain of a prevalent virus strain (GII.4). We report a highly selective transformation of asparagine 373, located in an antigenic loop adjoining the HBGA binding site, into an iso-aspartate residue. This spontaneous post-translational modification (PTM) proceeds with an estimated half-life of a few days at physiological temperatures, independent of the presence of HBGAs but dramatically affecting HBGA recognition. Sequence conservation and the surface-exposed position of this PTM suggest an important role in infection and immune recognition for many norovirus strains.

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Organizational Affiliation: 
• Institute of Chemistry and Metabolomics, Center of Structural and Cell Biology in Medicine (CSCM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany.
Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251, Hamburg, Germany.
Interfaculty Institute of BiochemistryUniversity of Tübingen, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076, Tübingen, Germany.
Faculty of Pharmacy, Institute of Chemistry, San Pablo CEU University, Urb. Montepríncipe, 28668, Boadilla del Monte, Spain.
Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, 2100, Denmark.
Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
Institute of Chemistry and Metabolomics, Center of Structural and Cell Biology in Medicine (CSCM), University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.49 kDa 
• Atom Count: 5,656 
• Modeled Residue Count: 612 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	309	Norovirus Hu/GII-4/Saga4/2006/JP	Mutation(s): 0
UniProt
Find proteins for B5BTR7 (Norovirus Hu/GII-4/Saga4/2006/JP) Explore B5BTR7  Go to UniProtKB:  B5BTR7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFU	C [auth A], E [auth B]	methyl alpha-L-fucopyranoside C7 H14 O5 OHWCAVRRXKJCRB-CXNFULCWSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free:  0.183 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.29	α = 90
b = 83.95	β = 95.78
c = 65.13	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Meyer, P.H.O., Blaum, B.S.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	BL1294/3-1

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary