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- PDB-6crj: Mouse norovirus model using the crystal structure of MNV P domain... -

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Basic information

Entry
Database: PDB / ID: 6crj
TitleMouse norovirus model using the crystal structure of MNV P domain and the Norwalkvirus shell domain
ComponentsNorwalk virus, MNV-1 capsid protein chimeraNorovirus
KeywordsVIRUS / norovirus / mouse
Function / homology
Function and homology information


T=3 icosahedral viral capsid / virus-mediated perturbation of host defense response / 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
Capsid protein / Capsid protein VP1
Similarity search - Component
Biological speciesNorwalk virus
Murine norovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsSmith, T.J.
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structural basis for murine norovirus engagement of bile acids and the CD300lf receptor.
Authors: Christopher A Nelson / Craig B Wilen / Ya-Nan Dai / Robert C Orchard / Arthur S Kim / Roderick A Stegeman / Leon L Hsieh / Thomas J Smith / Herbert W Virgin / Daved H Fremont /
Abstract: Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric ...Murine norovirus (MNoV) is closely related to human norovirus (HNoV), an infectious agent responsible for acute gastroenteritis worldwide. Here we report the X-ray crystal structure of the dimeric MNoV VP1 protruding (P) domain in complex with its cellular receptor CD300lf. CD300lf binds the P domain with a 2:2 stoichiometry, engaging a cleft between the AB and DE loops of the P2 subdomain at a site that overlaps the epitopes of neutralizing antibodies. We also identify that bile acids are cofactors enhancing MNoV cell-binding and infectivity. Structures of CD300lf-P domain in complex with glycochenodeoxycholic acid (GCDCA) and lithocholic acid (LCA) reveal two bile acid binding sites at the P domain dimer interface distant from receptor binding sites. The structural determinants for receptor and bile acid binding are supported by numerous biophysical assays utilizing interface residue mutations. We find that the monomeric affinity of CD300lf for the P domain is low and is divalent cation dependent. We have also determined the crystal structure of CD300lf in complex with phosphocholine, revealing that MNoV engages its receptor in a manner mimicking host ligands including similar metal coordination. Docking of the cocomplex structures onto a cryo-EM-derived model of MNoV suggests that each virion can make multiple CD300lf engagements, and thus, infection may be driven by the avidity of cell surface clustered CD300lf. These studies identify multiple potential modulators of norovirus infection that may act to regulate the interaction between the viral capsid P domain and its cognate cellular receptor.
#1: Journal: J Virol / Year: 2010
Title: High-resolution cryo-electron microscopy structures of murine norovirus 1 and rabbit hemorrhagic disease virus reveal marked flexibility in the receptor binding domains.
Authors: Umesh Katpally / Neil R Voss / Tommaso Cavazza / Stefan Taube / John R Rubin / Vivienne L Young / Jeanne Stuckey / Vernon K Ward / Herbert W Virgin / Christiane E Wobus / Thomas J Smith /
Abstract: Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. ...Our previous structural studies on intact, infectious murine norovirus 1 (MNV-1) virions demonstrated that the receptor binding protruding (P) domains are lifted off the inner shell of the virus. Here, the three-dimensional (3D) reconstructions of recombinant rabbit hemorrhagic disease virus (rRHDV) virus-like particles (VLPs) and intact MNV-1 were determined to approximately 8-A resolution. rRHDV also has a raised P domain, and therefore, this conformation is independent of infectivity and genus. The atomic structure of the MNV-1 P domain was used to interpret the MNV-1 reconstruction. Connections between the P and shell domains and between the floating P domains were modeled. This observed P-domain flexibility likely facilitates virus-host receptor interactions.
History
DepositionMar 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
B: Norwalk virus, MNV-1 capsid protein chimera
A: Norwalk virus, MNV-1 capsid protein chimera
C: Norwalk virus, MNV-1 capsid protein chimera


Theoretical massNumber of molelcules
Total (without water)171,3833
Polymers171,3833
Non-polymers00
Water0
1
B: Norwalk virus, MNV-1 capsid protein chimera
A: Norwalk virus, MNV-1 capsid protein chimera
C: Norwalk virus, MNV-1 capsid protein chimera
x 60


Theoretical massNumber of molelcules
Total (without water)10,282,954180
Polymers10,282,954180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Norwalk virus, MNV-1 capsid protein chimera
A: Norwalk virus, MNV-1 capsid protein chimera
C: Norwalk virus, MNV-1 capsid protein chimera
x 5


  • icosahedral pentamer
  • 857 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)856,91315
Polymers856,91315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: Norwalk virus, MNV-1 capsid protein chimera
A: Norwalk virus, MNV-1 capsid protein chimera
C: Norwalk virus, MNV-1 capsid protein chimera
x 6


  • icosahedral 23 hexamer
  • 1.03 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,028,29518
Polymers1,028,29518
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Norwalk virus, MNV-1 capsid protein chimera / Norovirus / CP / p59 / ORF2


Mass: 57127.523 Da / Num. of mol.: 3
Fragment: Norwalk shell domain (UNP residues 10-221), MNV-1 P domain (UNP residues 228-540)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus, (gene. exp.) Murine norovirus 1
Gene: ORF2 / Production host: Mus abbotti (Abbott's mouse) / References: UniProt: Q83884, UniProt: Q2V8W4

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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

ComponentName: mouse norovirus model / Type: VIRUS
Details: chimera of Norwalk virus shell domain and MNV P domain
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Murine norovirus 1
Source (recombinant)Organism: Mus abbotti (Abbott's mouse)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mus
Buffer solutionpH: 7.2 / Details: PBS
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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 10 e/Å2 / Film or detector model: FEI EAGLE (2k x 2k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 20425 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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