8Y5V | pdb_00008y5v

GII.4 Sydney PD and 2'-FL

• PDB DOI: https://doi.org/10.2210/pdb8Y5V/pdb

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


• Deposited: 2024-02-01 Released: 2024-06-19 
• Deposition Author(s): Hansman, G., Tame, J.R.H., Kher, G., Pancera, M.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Human milk oligosaccharide 2'-fucosyllactose guards norovirus histo-blood group antigen co-factor binding site.

Rudd, P.A., Kher, G., Tame, J.R.H., Irie, H., Haselhorst, T., von Itzstein, M., Pancera, M., Hansman, G.S.

(2024) J Virol 98: e0086524-e0086524

• PubMed: 38953656 
• DOI: https://doi.org/10.1128/jvi.00865-24
• Primary Citation Related Structures: 
  8Y5V, 8Y6C, 8Y6D

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Organizational Affiliation: 
• Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan.
School of Environment and Science, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.02 kDa 
• Atom Count: 2,766 
• Modeled Residue Count: 308 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GII.4 Sydney PD in complex with 2'-FL (powder)	A	309	Norovirus	Mutation(s): 0
UniProt
Find proteins for K4LM89 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU) Explore K4LM89  Go to UniProtKB:  K4LM89

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B [auth C]	3		N/A
Glycosylation Resources
GlyTouCan: G94133JU GlyCosmos: G94133JU GlyGen: G94133JU

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.624	α = 90
b = 55.763	β = 120.14
c = 63.613	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Hansman, G., Tame, J.R.H., Kher, G., Pancera, M.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2025-01-01
  Changes: Database references, Structure summary