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- EMDB-81567: Cryo-EM overall map of the GII.3 VLP in the resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-81567
TitleCryo-EM overall map of the GII.3 VLP in the resting state
Map dataCryo-EM overall map of the GII.3 VLP in the resting state
Sample
  • Virus: Norovirus Hu/Texas/TCH04-577/2004/US
    • Protein or peptide: HuNoV GII.3 TCH04-577 strain VP1
KeywordsCalicivirus / Molecular Interactions / Icosahedral Virus / Virus Like Particle / VIRUS
Biological speciesNorovirus Hu/Texas/TCH04-577/2004/US
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsSong C / Murata K
Funding support Korea, Republic Of, Japan, 4 items
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, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_81567.png

Downloads & links

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Map

FileDownload / File: emd_81567.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM overall map of the GII.3 VLP in the resting state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.021089528 - 0.027518464
Average (Standard dev.)0.000060706414 (±0.0011835803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 2 of the GII.3 resting-state overall map

Fileemd_81567_half_map_1.map
AnnotationHalf map 2 of the GII.3 resting-state overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of the GII.3 resting-state overall map

Fileemd_81567_half_map_2.map
AnnotationHalf map 1 of the GII.3 resting-state overall map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Norovirus Hu/Texas/TCH04-577/2004/US

EntireName: Norovirus Hu/Texas/TCH04-577/2004/US
Components
  • Virus: Norovirus Hu/Texas/TCH04-577/2004/US
    • Protein or peptide: HuNoV GII.3 TCH04-577 strain VP1

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Supramolecule #1: Norovirus Hu/Texas/TCH04-577/2004/US

SupramoleculeName: Norovirus Hu/Texas/TCH04-577/2004/US / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 479952 / Sci species name: Norovirus Hu/Texas/TCH04-577/2004/US / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: HuNoV GII.3 TCH04-577 strain VP1

MacromoleculeName: HuNoV GII.3 TCH04-577 strain VP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Norovirus Hu/Texas/TCH04-577/2004/US
SequenceString: MKMASNDATP SNDGAAGLVP EINNEAMALD PVAGAAIAAP LTGQQNIIDP WIMNNFVQAP GGEFTVSPRN SPGEVLLNLE LGPEINPYLA HLARMYNGYA GGFEVQVVLA GNAFTAGKII FAAIPPNFPI DNLSARQITM CPHVIVDVRQ LEPVNLPMPD VRNNFFHYNQ ...String:
MKMASNDATP SNDGAAGLVP EINNEAMALD PVAGAAIAAP LTGQQNIIDP WIMNNFVQAP GGEFTVSPRN SPGEVLLNLE LGPEINPYLA HLARMYNGYA GGFEVQVVLA GNAFTAGKII FAAIPPNFPI DNLSARQITM CPHVIVDVRQ LEPVNLPMPD VRNNFFHYNQ GSDSRLRLIA MLYTPLRANN SGDDVFTVSC RVLTRPSPDF SFNFLVPPTV ESKTKPFTLP ILTISEMSNS RFPVPIDSLH TSPTENIVVQ CQNGRVTLDG ELMGTTQLLP SQICAFMGVL TRSTSRASDQ ADTATPRLFN YYWHIQLDNP NGTPYDPAED IPGPLGTPDF RGKVFGVASQ RNPDSTTRAH EAKVDTTAGR FTPKLGSLEI STESDDFHQN QPTRFTPVGI GVDNEADFQQ WSLPDYSGQF THNMNLAPAV APNFPGEQLL FFRSQLPSSG GRSNGILDCL VPQEWVQHFY QESAPSQTQV ALVRYVNPDT GRVLFEAKLH KLGFMTIAKN GDSPITVPPN GYFRFESWVN PFYTLAPMGT GNGRRRIQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 18996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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