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Basic information

Entry
Database: EMDB / ID: EMD-71603
TitleCryo-EM structure of VX93 Fab in complex with GII.4 Norovirus P domain
Map datastructure of VX93 Fab in complex with GII.4 Norovirus P domain
Sample
  • Complex: VX93 Fab in complex with GII.4 Norovirus P domain
    • Protein or peptide: VP1
    • Protein or peptide: VX93 heavy chain
    • Protein or peptide: VX93 light chain
KeywordsNorovirus / Antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesHomo sapiens (human) / Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsJo G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: To Be Published
Title: Serum IgA proteomics reveals clonal composition and neutralization of dimeric and monomeric IgA repertoires against human norovirus
Authors: Jo G / Ward AB
History
DepositionJul 4, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71603.png

Downloads & links

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Map

FileReleased
Annotationstructure of VX93 Fab in complex with GII.4 Norovirus P domain
Voxel sizeX=Y=Z: 0.725 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.08108059 - 0.13746543
Average (Standard dev.)0.000016849162 (±0.0024436135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 304.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : VX93 Fab in complex with GII.4 Norovirus P domain

EntireName: VX93 Fab in complex with GII.4 Norovirus P domain
Components
  • Complex: VX93 Fab in complex with GII.4 Norovirus P domain
    • Protein or peptide: VP1
    • Protein or peptide: VX93 heavy chain
    • Protein or peptide: VX93 light chain

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Supramolecule #1: VX93 Fab in complex with GII.4 Norovirus P domain

SupramoleculeName: VX93 Fab in complex with GII.4 Norovirus P domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 34.215129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPSKPFSVPV LTVEEMTNSR FPIPLEKLFT GPSSAFVVQP QNGRCTTDGV LLGTTQLSPV NICTFRGDVT HITGSRNYTM NLASQNWND YDPTEEIPAP LGTPDFVGKI QGVLTQTTRT DGSTRGHKAT VYTGSADFAP KLGRVQFETD TDRDFEANQN T KFTPVGVI ...String:
GPSKPFSVPV LTVEEMTNSR FPIPLEKLFT GPSSAFVVQP QNGRCTTDGV LLGTTQLSPV NICTFRGDVT HITGSRNYTM NLASQNWND YDPTEEIPAP LGTPDFVGKI QGVLTQTTRT DGSTRGHKAT VYTGSADFAP KLGRVQFETD TDRDFEANQN T KFTPVGVI QDGGTTHRNE PQQWVLPSYS GRNTHNVHLA PAVAPTFPGE QLLFFRSTMP GCSGYPNMDL DCLLPQEWVQ YF YQEAAPA QSDVALLRFV NPDTGRVLFE CKLHKSGYVT VAHTGQHDLV IPPNGYFRFD SWVNQFYTLA PM

UniProtKB: VP1

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Macromolecule #2: VX93 heavy chain

MacromoleculeName: VX93 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.104677 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG LVKPSQTLSL TCTVSGVFIR TGGYYWTWIR HRPGKGLEWI GHVYYNGDSF YNPSLESRVA ISVDTSKNQF SLRLHSVTA ADTAEYFCVR GWFSSSYYRL DYFDSWGQGA QVTVSP

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Macromolecule #3: VX93 light chain

MacromoleculeName: VX93 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.571962 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPDS LAVSLGERAT INCKSSQSIF YSSNNKNYLA WYQKKPGQPP KQIFYWASTR ESGVPDRFTG SGSGTDFTLT INSLQAEDV AVYYCQQYYS IPLTFGPGTK VDIK

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3620 / Average exposure time: 3.03 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC - ab initio
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 332242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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