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- EMDB-44673: Norovirus GI.1 VLP bound to 16E10 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-44673
TitleNorovirus GI.1 VLP bound to 16E10 Fab
Map data
Sample
  • Complex: Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrically bound to 16E10 Fab
    • Complex: Icosahedral VLP of norovirus GI.1 VP1
    • Complex: Fab fragment of antibody 16E10
Keywordsnorovirus / VLP / antibody / VIRUS LIKE PARTICLE
Biological speciesNorovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsOlia AS / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Microbiol / Year: 2025
Title: A broadly protective human antibody for GI genogroup noroviruses.
Authors: Inga Rimkute / Adam S Olia / Mehin Suleiman / Kamron D Woods / Tatsiana Bylund / Nicholas C Morano / Ena S Tully / Raffaello Verardi / Saran Bao / Margaret H Beddall / Natthawan Chaimongkol ...Authors: Inga Rimkute / Adam S Olia / Mehin Suleiman / Kamron D Woods / Tatsiana Bylund / Nicholas C Morano / Ena S Tully / Raffaello Verardi / Saran Bao / Margaret H Beddall / Natthawan Chaimongkol / Mitzi M Donaldson / Renguang Du / Caitlyn N M Dulan / Jason Gorman / Amy R Henry / Chaim A Schramm / Stanislav V Sosnovtsev / Tyler Stephens / John-Paul Todd / Yaroslav Tsybovsky / Daniel C Douek / Kim Y Green / Reda Rawi / Lawrence Shapiro / Tongqing Zhou / Peter D Kwong / Mario Roederer /
Abstract: Noroviruses infect millions each year, and while effective countermeasures are eagerly sought, none have been reported for the GI genogroup, first described more than 50 years ago. Here, to provide ...Noroviruses infect millions each year, and while effective countermeasures are eagerly sought, none have been reported for the GI genogroup, first described more than 50 years ago. Here, to provide insight into GI norovirus neutralization, we isolated a broad GI antibody, 16E10, from a human blood donor and showed it neutralizes noroviruses in human enteroid cultures and abrogates or reduces infection in rhesus macaques. The cryogenic electron microscopy reconstruction of 16E10 with a norovirus protruding-domain dimer at 2.56-Å resolution reveals an exceptionally large binding surface, overlapping an antibody supersite, distal from host receptor-binding or cofactor-binding sites. Cryogenic electron microscopy reconstructions with virus-like particles (VLPs) showed that 16E10 disrupts protruding domains on the VLP surface and disassembles VLPs, altering viral organization required for avidity. While its epitope was generally conserved, 16E10 recognized multiple sequence-divergent residues, binding to which was enabled by corresponding cavities in the 16E10-norovirus interface. Broad recognition of noroviruses can thus incorporate sequence-divergent residues, through a cavity-based mechanism of diversity tolerance.
History
DepositionMay 1, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44673.png

Downloads & links

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Map

FileDownload / File: emd_44673.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.27398148 - 0.8662162
Average (Standard dev.)0.005714455 (±0.038284495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44673_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: #2

Fileemd_44673_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrical...

EntireName: Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrically bound to 16E10 Fab
Components
  • Complex: Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrically bound to 16E10 Fab
    • Complex: Icosahedral VLP of norovirus GI.1 VP1
    • Complex: Fab fragment of antibody 16E10

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Supramolecule #1: Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrical...

SupramoleculeName: Icosahedral virus-like particle of norovirus GI.1 VP1 symmetrically bound to 16E10 Fab
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Norovirus
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: Icosahedral VLP of norovirus GI.1 VP1

SupramoleculeName: Icosahedral VLP of norovirus GI.1 VP1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Norovirus

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Supramolecule #3: Fab fragment of antibody 16E10

SupramoleculeName: Fab fragment of antibody 16E10 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58007
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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