5IYP | pdb_00005iyp

Protruding domain of GII.4 human norovirus CHDC2094 in complex with HBGA type A (triglycan)

• PDB DOI: https://doi.org/10.2210/pdb5IYP/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: 1.27 Å
• R-Value Free: 
  0.159 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.136 (Depositor) 

Starting Model: experimental

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: 69.17 kDa 
• Atom Count: 5,823 
• 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-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan: G15611BA GlyCosmos: G15611BA GlyGen: G15611BA

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.159 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.135 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.136 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.71	α = 90
b = 106.12	β = 90
c = 135.92	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: 2017-04-05 
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