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- EMDB-76763: M6 bound to A-A' VP1 dimer of GII.4 Syd VLP: other side (T=1) -

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Basic information

Entry
Database: EMDB / ID: EMD-76763
TitleM6 bound to A-A' VP1 dimer of GII.4 Syd VLP: other side (T=1)
Map data
Sample
  • Virus: Norovirus
    • Protein or peptide: VP1
    • Protein or peptide: M6
KeywordsNorovirus / Sydney / VLP / Capsid / Antibody / VIRUS LIKE PARTICLE
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU / Lama glama (llama) / Norovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsApostol CV / Anish R / Pham S / Prasad BVV
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
CitationJournal: Res Sq / Year: 2026
Title: Symmetry-breaking antibody binding reveals extensive capsid malleability in pandemic human norovirus.
Authors: Carmen V Apostol / Ramakrishnan Anish / Son Pham / Khalil Ettayebi / Janam Dave / Frederick H Neill / Marina Bok / Banumathi Sankaran / Sue Crawford / Robert L Atmar / James E Crowe / ...Authors: Carmen V Apostol / Ramakrishnan Anish / Son Pham / Khalil Ettayebi / Janam Dave / Frederick H Neill / Marina Bok / Banumathi Sankaran / Sue Crawford / Robert L Atmar / James E Crowe / Viviana Parreño / Mary K Estes / B V Venkataram Prasad /
Abstract: Virus capsids are metastable assemblies with an exquisite balance between stability and flexibility, obligatory for entry, infectivity, and immune escape. Yet, the extent to which human viruses ...Virus capsids are metastable assemblies with an exquisite balance between stability and flexibility, obligatory for entry, infectivity, and immune escape. Yet, the extent to which human viruses exploit capsid plasticity and how that consequently shapes antigenic landscapes remains poorly understood. Human noroviruses (HuNoVs) are the leading cause of acute viral gastroenteritis worldwide. GII.4 HuNoVs have been evolving epochally, driving most global pandemics, and since 2012, GII.4 Sydney has been the dominant variant. The major capsid protein VP1 is central to infectivity and immune recognition, and VP1-based virus-like particles (VLPs) are considered promising vaccine candidates. Yet, how the icosahedral HuNoV capsid responds to antibody pressure at the atomic level is still unclear. Here, we present the first atomic structure of GII.4 Sydney capsid determined by cryo-EM, revealing the structural features that likely contribute to its sustained dominance. Using focused refinement, we uncovered the remarkable capsid plasticity in response to symmetry-breaking binding of neutralizing and non-neutralizing antibodies. VP1 adopts 11 distinct conformational modalities to accommodate asymmetric antibody binding, and antibody-disrupted VLPs reassemble into smaller particles with five additional VP1 states. This previously unrecognized extent of conformational adaptability provides key insights for designing next-generation VLP- or mRNA-based vaccines targeting HuNoV infections.
History
DepositionApr 18, 2026-
Header (metadata) releaseOct 28, 2026-
Map releaseOct 28, 2026-
UpdateOct 28, 2026-
Current statusOct 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76763.png

Downloads & links

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Map

FileDownload / File: emd_76763.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å		1.08 Å/pix.
x 560 pix.
= 604.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.3541753 - 0.72843075
Average (Standard dev.)0.00014653627 (±0.0066410108)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 604.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76763_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76763_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Norovirus

EntireName: Norovirus
Components
  • Virus: Norovirus
    • Protein or peptide: VP1
    • Protein or peptide: M6

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Supramolecule #1: Norovirus

SupramoleculeName: Norovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 142786 / Sci species name: Norovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Virus shellShell ID: 1 / Name: VP1 / Diameter: 420.0 Å / T number (triangulation number): 3

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Molecular weightTheoretical: 54.022469 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QNVIDPWIRN NFVQAPGGEF TVSPRNAPGE ILWSAPLGPD LNPYLSHLAR MYNGYAGGFE VQVILAGNAF TAGKVIFAAV PPNFPTEGL SPSQVTMFPH IVVDVRQLEP VLIPLPDVRN NFYHYNQSND PTIKLIAMLY TPLRANNAGD DVFTVSCRVL T RPSPDFDF ...String:
QNVIDPWIRN NFVQAPGGEF TVSPRNAPGE ILWSAPLGPD LNPYLSHLAR MYNGYAGGFE VQVILAGNAF TAGKVIFAAV PPNFPTEGL SPSQVTMFPH IVVDVRQLEP VLIPLPDVRN NFYHYNQSND PTIKLIAMLY TPLRANNAGD DVFTVSCRVL T RPSPDFDF IFLVPPTVES RTKPFSVPVL TVEEMTNSRF PIPLEKLFTG PSSAFVVQPQ NGRCTTDGVL LGTTQLSPVN IC TFRGDVT HITGSRNYTM NLASQNWNDY DPTEEIPAPL GTPDFVGKIQ GVLTQTTRTD GSTRGHKATV YTGSADFAPK LGR VQFETD TDRDFEANQN TKFTPVGVIQ DGGTTHRNEP QQWVLPSYSG RNTHNVHLAP AVAPTFPGEQ LLFFRSTMPG CSGY PNMDL DCLLPQEWVQ YFYQEAAPAQ SDVALLRFVN PDTGRVLFEC KLHKSGYVTV AHTGQHDLVI PPNGYFRFDS WVNQF YTLA PMGN

UniProtKB: VP1

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Macromolecule #2: M6

MacromoleculeName: M6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.180483 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
VKLQESGGGL VQAGESLRLS CAASGSNFSI NGVGWYRQAP GKQRELVAGI TNGGYTSYAD SVKGRFTIST DNAKNTVYLQ MNSLRPEDT AVYYCNANFQ IHRSGADYVR NYWGQGTQVT VSA

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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: 6 / Details: 1X PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 3290 / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie mode at 35 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v4.7.0) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

12qz

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.7.0) / Number images used: 399653
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.7.0)
FSC plot (resolution estimation)

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