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- PDB-27zd: Human norovirus GII.3 TCH04-577 VP1 -

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Entry
Database: PDB / ID: 27zd
TitleHuman norovirus GII.3 TCH04-577 VP1
ComponentsHuman norovirus GII.3 TCH04-577 VP1
KeywordsVIRUS / Calicivirus / Molecular Interactions / Icosahedral Virus / Virus Like Particle
Biological speciesNorovirus Hu/Texas/TCH04-577/2004/US
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSong, C. / Murata, K.
Funding support Korea, Republic Of, Japan, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00440289 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2026-25476185 Korea, Republic Of
Japan Agency for Medical Research and Development (AMED)JP24ama121005 Japan
Japan Agency for Medical Research and Development (AMED)JP25ama121005 Japan
CitationJournal: Int J Mol Sci / Year: 2026
Title: Conformational Plasticity of the Human Norovirus GII.3 Capsid Reveals Alternative P Domain Interaction Networks.
Authors: Chihong Song / Motohiro Miki / Reiko Takai-Todaka / Kosuke Murakami / Kazuhiko Katayama / Kazuyoshi Murata /
Abstract: Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide, yet no effective antiviral therapeutics are currently available. Although environmentally induced capsid ...Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide, yet no effective antiviral therapeutics are currently available. Although environmentally induced capsid conformational changes associated with infectivity have been reported in murine noroviruses (MNVs), comparable conformational switching has not been demonstrated in HuNoVs. In this study, we generated HuNoV GII.3 virus-like particles (VLPs) using a baculovirus expression system and identified two distinct T = 3 particle populations coexisting within VLP preparations derived from a single strain through cryo-electron microscopy single-particle analysis. Comparative structural analysis revealed that these two T = 3 capsid conformations correspond to the resting and rising states of the protruding (P) domain. Rearrangement of the P domain alters intermolecular interactions between adjacent capsid subunits, resulting in distinct capsid surface architectures. In the resting state, intermolecular contacts were mediated predominantly by the P2 subdomain, with limited contribution from the P1 subdomain. In contrast, the rising state exhibited a shift toward an alternative interaction interface primarily involving the P1 subdomain. The alteration of the capsid surface accompanying this conformational switching can influence biologically relevant intermolecular interactions with viral hosts and antibodies as demonstrated in murine norovirus. These findings demonstrate previously unrecognized structural polymorphism in the HuNoV capsid and provide evidence that conformational switching may occur in HuNoVs. Our results offer new insights into norovirus capsid dynamics and may inform future structure-based vaccine and antiviral drug development.
History
DepositionJun 18, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human norovirus GII.3 TCH04-577 VP1
B: Human norovirus GII.3 TCH04-577 VP1
C: Human norovirus GII.3 TCH04-577 VP1


Theoretical massNumber of molelcules
Total (without water)180,3193
Polymers180,3193
Non-polymers00
Water00
1
A: Human norovirus GII.3 TCH04-577 VP1
B: Human norovirus GII.3 TCH04-577 VP1
C: Human norovirus GII.3 TCH04-577 VP1
x 60


Theoretical massNumber of molelcules
Total (without water)10,819,146180
Polymers10,819,146180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Human norovirus GII.3 TCH04-577 VP1


Mass: 60106.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/Texas/TCH04-577/2004/US / Production host: unidentified baculovirus
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Norovirus Hu/Texas/TCH04-577/2004/US / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Norovirus Hu/Texas/TCH04-577/2004/US
Source (recombinant)Organism: unidentified baculovirus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 0 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION4particle selection
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8498 / Symmetry type: POINT

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