5BSY | pdb_00005bsy

Crystal structure of GII.10 P domain in complex with lemon juice

PDB DOI: https://doi.org/10.2210/pdb5BSY/pdb

Classification: VIRAL PROTEIN
Organism(s): Norwalk virus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-06-02 Released: 2015-09-09
Deposition Author(s): Koromyslova, A.D., Hansman, G.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.196 (DCC)
R-Value Work:
0.160 (Depositor), 0.170 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Treatment of norovirus particles with citrate.

Koromyslova, A.D., White, P.A., Hansman, G.S.

(2015) Virology 485: 199-204

PubMed: 26295280 Search on PubMed
DOI: https://doi.org/10.1016/j.virol.2015.07.009
Primary Citation Related Structures:
5BSX, 5BSY

PubMed Abstract:
Human norovirus is a dominant cause of acute gastroenteritis around the world. Several norovirus disinfectants label citric acid as an active ingredient. In this study, we showed that norovirus virus-like particles (VLPs) treated with citrate buffer caused the particles to alter their morphology, including increased diameters associated with a new ring-like structure. We also found that epitopes on the protruding (P) domain on these particles were more readily accessible to antibodies after the citrate treatment. These results suggested that citrate had a direct effect on the norovirus particles. Using X-ray crystallography, we showed that the P domain bound citrate from lemon juice and a disinfectant containing citric acid. Importantly, citrate binds at the histo-blood group antigen binding pocket, which are attachment factors for norovirus infections. Taken together, these new findings suggested that it might be possible to treat/reduce norovirus infections with citrate, although further studies are needed.

Organizational Affiliation

Schaller Research Group at the University of Heidelberg and the DKFZ, Heidelberg 69120, Germany; Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg 69120, Germany.

Macromolecule Content

Total Structure Weight: 69.57 kDa
Atom Count: 5,548
Modeled Residue Count: 624
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B	315	Norwalk virus	Mutation(s): 0
UniProt
Find proteins for Q5F4T5 (Norwalk virus) Explore Q5F4T5 Go to UniProtKB: Q5F4T5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5F4T5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]