PXD019884

PXD019884 is an original dataset announced via ProteomeXchange.

Title	Glycan-induced structural dynamics in human norovirus P dimers depend on the virus strain and deamidation status
Description	Noroviruses are non-enveloped (+) single stranded RNA viruses of the Caliciviridae family that cause an estimated 20 % of gastroenteritis cases worldwide . The virus possesses an icosahedral capsid, build by the two structural proteins VP1 and VP2. Noroviruses of genogroup II, especially GII.4, dominated in the majorities of outbreaks in the last two decades. In the last years, a novel GII.17 strain has also emerged in Asia. The major capsid protein VP1 builds dimers that are divided into the inner shell (S) domain and the outward-facing protruding (P) domain. The P domain is further divided into P1 and P2 subdomains, of which P2 is essential for host immune response and binds to histo blood-group antigens (HBGAs) for cell attachment in a strain-dependent manner, but the exact mechanism of cell attachment and entry remains unclear. Recently, a spontaneous deamidation of N373 with subsequent formation of an iso-aspartate (iD) was identified in GII.4 Saga P dimers that strongly attenuates glycan binding. This deamidation appears to be site specific and occurs in GII.4 MI001 P dimers as well, whereas it is absent in GII.10 Vietnam 026 and GII.17 Kawasaki 308 P dimers, which carry an Asp at the equivalent position. Given their high structural similarity with at the same time strain-dependent glycan binding behavior, we wanted to study if glycan binding induces different dynamic changes in P dimers of different strains using Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Furthermore, we wanted to examine the structural effects of fucose binding to a mixture of wildtype and deamidated GII.4 MI001 and GII.4 Saga P dimers, to get more insights about the dynamic changes induced by N373 deamidation. Our results suggest identical glycan binding behavior of the almost identical GII.4 Saga and GII.4 MI001 strains, but reveal different glycan induced dynamics in GII.17 Kawasaki 308 and GII.10 Vietnam 026. Furthermore, all strains apart from GII.4 Saga form a second P domain species that is highly protected from HDX . In mixtures of wildtype and N373 deamidated GII.4 P dimers, fucose binding leads to different structural dynamics than in pure wildtype, indicating that the deamidated species could have a biological function in vivo.
HostingRepository	PRIDE
AnnounceDate	2021-04-08
AnnouncementXML	Submission_2021-04-07_23:55:25.312.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jasmin Dülfer
SpeciesList	scientific name: Norovirus Hu/GII.4/MI001/2011/USA; NCBI TaxID: 1354724; scientific name: Norovirus Hu/GII/JP/2015/GII.P17_GII.17/Kawasaki308; NCBI TaxID: 1634342; scientific name: Norovirus Hu/GII.4/Saga4/2009/JP; NCBI TaxID: 1498751; scientific name: Norwalk virus; NCBI TaxID: 11983;
ModificationList	deamidated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-18 23:00:13	ID requested
⏵ 1	2021-04-07 23:55:25	announced

Dataset with its publication pending

submitter keyword: norovirus, glycan, protein dynamics, interaction, deamidation, HDX-MS

Charlotte Uetrecht
contact affiliation	Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany European XFEL, Schenefeld, Germany
contact email	charlotte.uetrecht@xfel.eu
lab head
Jasmin Dülfer
contact affiliation	Heinrich Pette Institute
contact email	jasmin.duelfer@leibniz-hpi.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD019884
     1. Label: PRIDE project
     2. Name: Glycan-induced structural dynamics in human norovirus P dimers depend on the virus strain and deamidation status