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- EMDB-23187: Mouse Norovirus Protruding domain complexed with neutralizing Fab... -

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Basic information

Entry
Database: EMDB / ID: EMD-23187
TitleMouse Norovirus Protruding domain complexed with neutralizing Fab fragment from mAb A6.2
Map dataSoluble form of mouse norovirus protruding domain complexed with Fab fragments from neutralizing mAb A6.2
Sample
  • Complex: Murine norovirus 1 - Fab complex
    • Complex: Capsid protein
      • Protein or peptide: Capsid protein
    • Complex: Anti mouse norovirus mAb A6.2 Fab
      • Protein or peptide: Anti mouse norovirus mAb A6.2 Fab light chain
      • Protein or peptide: Anti mouse norovirus mAb A6.2 Fab heavy chain
KeywordsAntibody / norovirus / spike / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / antigenic variation / virion component / host cell cytoplasm
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 speciesMurine norovirus 1 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSmith TJ / Sherman MB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01-AI141465 United States
CitationJournal: J Virol / Year: 2021
Title: A Norovirus Uses Bile Salts To Escape Antibody Recognition While Enhancing Receptor Binding.
Authors: Alexis N Williams / Michael B Sherman / Hong Q Smith / Stefan Taube / B Montgomery Pettitt / Christiane E Wobus / Thomas J Smith /
Abstract: Noroviruses, members of the family, are the major cause of epidemic gastroenteritis in humans, causing ∼20 million cases annually. These plus-strand RNA viruses have T=3 icosahedral protein ...Noroviruses, members of the family, are the major cause of epidemic gastroenteritis in humans, causing ∼20 million cases annually. These plus-strand RNA viruses have T=3 icosahedral protein capsids with 90 pronounced protruding (P) domain dimers to which antibodies and cellular receptors bind. In the case of mouse norovirus (MNV), bile salts have been shown to enhance receptor (CD300lf) binding to the P domain. We demonstrated previously that the P domains of several genotypes are markedly flexible and "float" over the shell, but the role of this flexibility was unclear. Recently, we demonstrated that bile causes a 90° rotation and collapse of the P domain onto the shell surface. Since bile binds distally to the P-shell interface, it was not at all clear how it could cause such dramatic changes. Here, we present the near-atomic resolution cryo-electron microscopy (cryo-EM) structure of the MNV protruding domain complexed with a neutralizing Fab. On the basis of previous results, we show here that bile salts cause allosteric conformational changes in the P domain that block antibody recognition of the top of the P domain. In addition, bile causes a major rearrangement of the P domain dimers that is likely responsible for the bile-induced collapse of the P domain onto the shell. In the contracted shell conformation, antibodies to the P1 and shell domains are not expected to bind. Therefore, at the site of infection in the gut, the host's own bile allows the virus to escape antibody-mediated neutralization while enhancing cell attachment. The major feature of calicivirus capsids is the 90 protruding domains (P domains) that are the site of cell receptor attachment and antibody epitopes. We demonstrated previously that these P domains are highly mobile and that bile causes these "floating" P domains in mouse norovirus (MNV) to contract onto the shell surface. Here, we present the near-atomic cryo-EM structure of the isolated MNV P domain complexed with a neutralizing Fab fragment. Our data show that bile causes two sets of changes. First, bile causes allosteric conformational changes in the epitopes at the top of the P domain that block antibody binding. Second, bile causes the P domain dimer subunits to rotate relative to each other, causing a contraction of the P domain that buries epitopes at the base of the P and shell domains. Taken together, the results show that MNV uses the host's own metabolites to enhance cell receptor binding while simultaneously blocking antibody recognition.
History
DepositionDec 22, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.31
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.31
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7l5j
  • Surface level: 0.31
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23187.png

Downloads & links

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Map

FileDownload / File: emd_23187.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSoluble form of mouse norovirus protruding domain complexed with Fab fragments from neutralizing mAb A6.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31 / Movie #1: 0.31
Minimum - Maximum-1.7439922 - 2.7713642
Average (Standard dev.)0.0012879022 (±0.08286352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z217.600217.600217.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.7442.7710.001

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Supplemental data

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Sample components

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Entire : Murine norovirus 1 - Fab complex

EntireName: Murine norovirus 1 - Fab complex
Components
  • Complex: Murine norovirus 1 - Fab complex
    • Complex: Capsid protein
      • Protein or peptide: Capsid protein
    • Complex: Anti mouse norovirus mAb A6.2 Fab
      • Protein or peptide: Anti mouse norovirus mAb A6.2 Fab light chain
      • Protein or peptide: Anti mouse norovirus mAb A6.2 Fab heavy chain

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Supramolecule #1: Murine norovirus 1 - Fab complex

SupramoleculeName: Murine norovirus 1 - Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Capsid protein

SupramoleculeName: Capsid protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Murine norovirus 1

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Supramolecule #3: Anti mouse norovirus mAb A6.2 Fab

SupramoleculeName: Anti mouse norovirus mAb A6.2 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
Molecular weightTheoretical: 34.858281 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNATIYRMVD LPVIQPRLCT HARWPAPVYG LLVDPSLPSN PQWQNGRVHV DGTLLGTTPI SGSWVSCFAA EAAYEFQSGT GEVATFTLI EQDGSAYVPG DRAAPLGYPD FSGQLEIEVQ TETTKTGDKL KVTTFEMILG PTTNADQAPY QGRVFASVTA A ASLDLVDG ...String:
SNATIYRMVD LPVIQPRLCT HARWPAPVYG LLVDPSLPSN PQWQNGRVHV DGTLLGTTPI SGSWVSCFAA EAAYEFQSGT GEVATFTLI EQDGSAYVPG DRAAPLGYPD FSGQLEIEVQ TETTKTGDKL KVTTFEMILG PTTNADQAPY QGRVFASVTA A ASLDLVDG RVRAVPRSIY GFQDTIPEYN DGLLVPLAPP IGPFLPGEVL LRFRTYMRQI DTADAAAEAI DCALPQEFVS WF ASNAFTV QSEALLLRYR NTLTGQLLFE CKLYNEGYIA LSYSGSGPLT FPTDGIFEVV SWVPRLYQLA SVGSLATGRM LKQ

UniProtKB: Capsid protein

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Macromolecule #2: Anti mouse norovirus mAb A6.2 Fab light chain

MacromoleculeName: Anti mouse norovirus mAb A6.2 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.083512 KDa
SequenceString: QIVLTQSPAI MSASPGEKVT ITCSASSSVS YMHWFQQKPG TSPKLWIYST SNLASGVPAR FSGSGSGTSY SLTISRMEAE DAATYYCQQ RSSYPFTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
QIVLTQSPAI MSASPGEKVT ITCSASSSVS YMHWFQQKPG TSPKLWIYST SNLASGVPAR FSGSGSGTSY SLTISRMEAE DAATYYCQQ RSSYPFTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRN

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Macromolecule #3: Anti mouse norovirus mAb A6.2 Fab heavy chain

MacromoleculeName: Anti mouse norovirus mAb A6.2 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.759061 KDa
SequenceString: EVKLLESGGG LVQPGGSLKL SCAASGFDFS RYWMSWVRQA PGKGLEWIGQ INPHSSTINY TPSLRDKFII SRDNAKNTLY LQMTKVRSE DTALYYCARL LRYFYALDYW GQGASVTVSS AKTTPPSVYP LAPGRAAAAA SMVTLGCLVK GYFPEPVTVT W NSGSLAAG ...String:
EVKLLESGGG LVQPGGSLKL SCAASGFDFS RYWMSWVRQA PGKGLEWIGQ INPHSSTINY TPSLRDKFII SRDNAKNTLY LQMTKVRSE DTALYYCARL LRYFYALDYW GQGASVTVSS AKTTPPSVYP LAPGRAAAAA SMVTLGCLVK GYFPEPVTVT W NSGSLAAG VHTFPAVLQA ALYTLSSSVT VPSSSWPSET VTCNVAHPAS STKVDKKIVP RAA

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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: OTHER / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: OTHER
Details: Initial model was ab initio from hand picked particles.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1825383
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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