8VRV

GII.4c H2-tri HBGA norovirus protruding domain

• PDB DOI: https://doi.org/10.2210/pdb8VRV/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Norovirus GII.4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-22 Released: 2024-06-19 
• Deposition Author(s): Kher, G., Prewitt, A., Pancera, M., Hansman, G.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Advancement of norovirus therapies

Hansman, G., Kher, G.

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)

Macromolecule Content

• Total Structure Weight: 68.17 kDa 
• Atom Count: 5,453 
• Modelled Residue Count: 612 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	306	Norovirus GII.4	Mutation(s): 0
UniProt
Find proteins for A0A168DBN0 (Norovirus GII.4) Explore A0A168DBN0  Go to UniProtKB:  A0A168DBN0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G00068MO GlyCosmos:  G00068MO GlyGen:  G00068MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], F [auth B], G [auth B], I [auth B], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	E [auth A], H [auth B], L [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.666	α = 90
b = 90.47	β = 90
c = 91.339	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): Kher, G., Prewitt, A., Pancera, M., Hansman, G.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2327

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release