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- PDB-6iuk: Cryo-EM structure of Murine Norovirus capsid -

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Basic information

Entry
Database: PDB / ID: 6iuk
TitleCryo-EM structure of Murine Norovirus capsid
ComponentsMajor capsid protein VP1
KeywordsVIRUS / VLP / mature / stable
Function / homology
Function and homology information


virion component => GO:0044423 / host cell cytoplasm / 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 GV/NIH-2410/2005/USA
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSong, C. / Miyazaki, N. / Iwasaki, K. / Katayama, K. / Murata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0108034h0602 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072j0001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP26102545 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H00786 Japan
CitationJournal: PLoS Pathog / Year: 2020
Title: Dynamic rotation of the protruding domain enhances the infectivity of norovirus.
Authors: Chihong Song / Reiko Takai-Todaka / Motohiro Miki / Kei Haga / Akira Fujimoto / Ryoka Ishiyama / Kazuki Oikawa / Masaru Yokoyama / Naoyuki Miyazaki / Kenji Iwasaki / Kosuke Murakami / ...Authors: Chihong Song / Reiko Takai-Todaka / Motohiro Miki / Kei Haga / Akira Fujimoto / Ryoka Ishiyama / Kazuki Oikawa / Masaru Yokoyama / Naoyuki Miyazaki / Kenji Iwasaki / Kosuke Murakami / Kazuhiko Katayama / Kazuyoshi Murata /
Abstract: Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines ...Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the resting conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two similar P domain conformations were also found simultaneously in the human norovirus GII.3 capsid, although the mechanism of the conformational change is not yet clear. These results provide new insights into the mechanisms of non-enveloped norovirus transmission that invades host cells, replicates, and sometimes escapes the hosts immune system, through dramatic environmental changes in the gastrointestinal tract.
History
DepositionNov 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 27, 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

Movie
  • 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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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)176,5013
Polymers176,5013
Non-polymers00
Water0
1
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)10,590,081180
Polymers10,590,081180
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
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
x 5


  • icosahedral pentamer
  • 883 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)882,50715
Polymers882,50715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein VP1
B: Major capsid protein VP1
C: Major capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 1.06 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,059,00818
Polymers1,059,00818
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Major capsid protein VP1 /


Mass: 58833.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus GV/NIH-2410/2005/USA / Gene: VP1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: B7XA03

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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: Murine norovirus GV / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Murine norovirus GV
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM / Cell: RAW264.7 / Plasmid: cDNA
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Mus musculus
Virus shellDiameter: 400 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: amorphous ice
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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 / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 77 K / Temperature (min): 76 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2746
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 32 / Used frames/image: 3-31

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Processing

EM software
IDNameVersionCategory
2RELION2image acquisition
4CTFFIND4CTF correction
7Coot0.8.2model fitting
9PHENIX1.13model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41847 / Symmetry type: POINT
Atomic model buildingB value: 157 / Protocol: FLEXIBLE FIT / Space: REAL

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