5IYW | pdb_00005iyw

Protruding domain of GII.4 human norovirus CHDC2094 in complex with 3-fucosyllactose (3FL)

• PDB DOI: https://doi.org/10.2210/pdb5IYW/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Hu/GII.4/CHDC2094/1974/US
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-24 Released: 2017-04-05 
• Deposition Author(s): Singh, B.K., Hansman, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.171 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Starting Model: experimental

Literature

Structural basis for GII.4 norovirus inhibition by human milk oligosaccharides.

Singh, B.K., Hansman, G.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.78 kDa 
• Atom Count: 5,730 
• Modeled Residue Count: 609 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A, B	306	Norovirus Hu/GII.4/CHDC2094/1974/US	Mutation(s): 0
UniProt
Find proteins for D0QJ68 (Norovirus Hu/GII.4/CHDC2094/1974/US) Explore D0QJ68  Go to UniProtKB:  D0QJ68

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]alpha-D-glucopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G47920WV GlyCosmos: G47920WV GlyGen: G47920WV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	G [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.171 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.45	α = 90
b = 107.11	β = 90
c = 136.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Singh, B.K., Hansman, G.S.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, 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