5HZA

Crystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 FL)

• PDB DOI: https://doi.org/10.2210/pdb5HZA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus GII.10
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2016-02-02 Released: 2016-03-02 
• Deposition Author(s): Hansman, G.S., Koromyslova, A.D., Singh, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides.

Weichert, S., Koromyslova, A., Singh, B.K., Hansman, S., Jennewein, S., Schroten, H., Hansman, G.S.

(2016) J Virol 90: 4843-4848

• PubMed: 26889023 
• DOI: https://doi.org/10.1128/JVI.03223-15
• Primary Citation of Related Structures:  
  5HZA, 5HZB


• PubMed Abstract: 
  

  Histo-blood group antigens (HBGAs) are important binding factors for norovirus infections. We show that two human milk oligosaccharides, 2'-fucosyllactose (2'FL) and 3-fucosyllactose (3FL), could block norovirus from binding to surrogate HBGA samples. We found that 2'FL and 3FL bound at the equivalent HBGA pockets on the norovirus capsid using X-ray crystallography. Our data revealed that 2'FL and 3FL structurally mimic HBGAs. These results suggest that 2'FL and 3FL might act as naturally occurring decoys in humans.

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Organizational Affiliation: 

Pediatric Infectious Diseases Unit, University Children's Hospital Mannheim, University of Heidelberg, Mannheim, Germany.

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: 70.18 kDa 
• Atom Count: 5,750 
• Modelled Residue Count: 621 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	315	Norovirus GII.10	Mutation(s): 0
UniProt
Find proteins for Q5F4T5 (Norwalk virus) Explore Q5F4T5  Go to UniProtKB:  Q5F4T5

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G57548NB GlyCosmos:  G57548NB GlyGen:  G57548NB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.179 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.71	α = 90
b = 78.17	β = 102.3
c = 71.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Hansman, G.S., Koromyslova, A.D., Singh, B.K.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary