5LFE

Protruding domain of GII.4 human norovirus isolate 8-14 in complex with HBGA type B (triglycan)

• PDB DOI: https://doi.org/10.2210/pdb5LFE/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-01 Released: 2017-07-12 
• Deposition Author(s): Singh, B.K., Hansman, G.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 

Literature

Four decades of structural evolution of GII.4 norovirus

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: 68.88 kDa 
• Atom Count: 5,131 
• Modelled Residue Count: 615 
• 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/Sydney/NSW0514/2012/AU	Mutation(s): 0
UniProt
Find proteins for M4QNL3 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU) Explore M4QNL3  Go to UniProtKB:  M4QNL3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G11065GA GlyCosmos:  G11065GA GlyGen:  G11065GA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.233 
• R-Value Observed: 0.235 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.83	α = 90
b = 55.42	β = 99.38
c = 87.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Singh, B.K., Hansman, G.S.

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• 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