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- EMDB-44734: 16E10 Fab bound to norovirus GI.1 P domain -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-44734
Title16E10 Fab bound to norovirus GI.1 P domain
Map data
Sample
  • Complex: P domain dimer bound by two copies of 16E10 Fab
    • Complex: P domain dimer from GI.1 norovirus
      • Protein or peptide: Capsid protein VP1
    • Complex: 16E10 Fab
      • Protein or peptide: 16E10 Light Chain
      • Protein or peptide: 16E10 Heavy Chain
Keywordsnorovirus / VP1 / P-domain / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesNorovirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsOlia AS / Morano NC / Shapiro L / 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 3, 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_44734.png

Downloads & links

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Map

FileDownload / File: emd_44734.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.24736898 - 0.5017555
Average (Standard dev.)0.000873665 (±0.017618582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44734_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44734_half_map_2.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 : P domain dimer bound by two copies of 16E10 Fab

EntireName: P domain dimer bound by two copies of 16E10 Fab
Components
  • Complex: P domain dimer bound by two copies of 16E10 Fab
    • Complex: P domain dimer from GI.1 norovirus
      • Protein or peptide: Capsid protein VP1
    • Complex: 16E10 Fab
      • Protein or peptide: 16E10 Light Chain
      • Protein or peptide: 16E10 Heavy Chain

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Supramolecule #1: P domain dimer bound by two copies of 16E10 Fab

SupramoleculeName: P domain dimer bound by two copies of 16E10 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Norovirus

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Supramolecule #2: P domain dimer from GI.1 norovirus

SupramoleculeName: P domain dimer from GI.1 norovirus / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Norovirus

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Supramolecule #3: 16E10 Fab

SupramoleculeName: 16E10 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Norovirus
Molecular weightTheoretical: 31.337105 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPKTRPFTLP NLPLSSLSNS RAPLPISSIG ISPDNVQSVQ FQNGRCTLDG RLVGTTPVSL SHVAKIRGTS NGTVINLTEL DGTPFHPFE GPAPIGFPDL GGCDWHINMT QFGHSSQTQY DVDTTPDTFV PHLGSIQANG IGSGNYVGVL SWISPPSHPS G SQVDLWKI ...String:
GPKTRPFTLP NLPLSSLSNS RAPLPISSIG ISPDNVQSVQ FQNGRCTLDG RLVGTTPVSL SHVAKIRGTS NGTVINLTEL DGTPFHPFE GPAPIGFPDL GGCDWHINMT QFGHSSQTQY DVDTTPDTFV PHLGSIQANG IGSGNYVGVL SWISPPSHPS G SQVDLWKI PNYGSSITEA THLAPSVYPP GFGEVLVFFM SKMPGPGAYN LPCLLPQEYI SHLASEQAPT VGEAALLHYV DP DTGRNLG EFKAYPDGFL TCVPNGASSG PQQLPINGVF VFVSWVSRFY QLKPVGT

UniProtKB: Capsid protein VP1

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Macromolecule #2: 16E10 Light Chain

MacromoleculeName: 16E10 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.908594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMSQSPVS LPVTPGEPAS ISCRSSQSLL HSNGYNYVDW YLQKPGQSPQ LLLYLGSNRA AGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTKL DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMSQSPVS LPVTPGEPAS ISCRSSQSLL HSNGYNYVDW YLQKPGQSPQ LLLYLGSNRA AGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTKL DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: 16E10 Heavy Chain

MacromoleculeName: 16E10 Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.514283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLLESGGAL VHPGGSLRLS CAASGFTFSS SSFSWVRQAP GKGLEWVSGI NPSGHDTYYA DSVKGRFTIS RDNSKDTLFL EMNSLRAED TAQYYCAKKI DFPFRGGRRY SDSRPYNTGS LDSWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
VQLLESGGAL VHPGGSLRLS CAASGFTFSS SSFSWVRQAP GKGLEWVSGI NPSGHDTYYA DSVKGRFTIS RDNSKDTLFL EMNSLRAED TAQYYCAKKI DFPFRGGRRY SDSRPYNTGS LDSWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKV

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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: 5
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: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 393251
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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