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- PDB-7l5j: Mouse Norovirus Protruding domain complexed with neutralizing Fab... -

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Basic information

Entry
Database: PDB / ID: 7l5j
TitleMouse Norovirus Protruding domain complexed with neutralizing Fab fragment from mAb A6.2
Components
  • Anti mouse norovirus mAb A6.2 Fab heavy chain
  • Anti mouse norovirus mAb A6.2 Fab light chain
  • Capsid proteinCapsid
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / norovirus / spike / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virus-mediated perturbation of host defense response / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological speciesMurine norovirus 1
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSmith, T.J. / Sherman, M.B.
Funding support United States, 1items
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, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
L: Anti mouse norovirus mAb A6.2 Fab light chain
W: Anti mouse norovirus mAb A6.2 Fab heavy chain
X: Anti mouse norovirus mAb A6.2 Fab light chain
Y: Anti mouse norovirus mAb A6.2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)163,4026
Polymers163,4026
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Assembly as was observed in our previous Fab complex with intact virion.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14220 Å2
ΔGint-81 kcal/mol
Surface area63650 Å2

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Components

#1: Protein Capsid protein / Capsid


Mass: 34858.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2V8W4
#2: Antibody Anti mouse norovirus mAb A6.2 Fab light chain


Mass: 23083.512 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Anti mouse norovirus mAb A6.2 Fab heavy chain


Mass: 23759.061 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Murine norovirus 1 - Fab complexCOMPLEXall0MULTIPLE SOURCES
2Capsid proteinCapsidCOMPLEX#11RECOMBINANT
3Anti mouse norovirus mAb A6.2 FabCOMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Murine norovirus 1223997
33Mus musculus (house mouse)10090
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Mus musculus
Virus shellName: Protein Icosahedron / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: OTHER

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Processing

SoftwareName: PHENIX / Version: 1.15_3448: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1825383 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811530
ELECTRON MICROSCOPYf_angle_d0.84815744
ELECTRON MICROSCOPYf_dihedral_angle_d10.8966826
ELECTRON MICROSCOPYf_chiral_restr0.0471771
ELECTRON MICROSCOPYf_plane_restr0.0052019

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