8Y5V

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 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

GII.4 Sydney PD and 2'-FL

Hansman, G., Tame, J.R.H., Kher, G., Pancera, M.

To be published.

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 
• Modelled 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	3D 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 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• 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