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- PDB-6s6l: Cryo-EM structure of murine norovirus (MNV-1) -

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Basic information

Entry
Database: PDB / ID: 6s6l
TitleCryo-EM structure of murine norovirus (MNV-1)
ComponentsCapsid protein
KeywordsVIRUS / Norovirus / Capsid / VP1
Function / homology
Function and homology information


virion component / :
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Jelly Rolls - #20 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnowden, J.S. / Hurdiss, D.L. / Adeyemi, O.O. / Ranson, N.A. / Herod, M.R. / Stonehouse, N.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
Wellcome Trust102572/B/13/Z United Kingdom
Medical Research Council (United Kingdom)MR/S007229/1 United Kingdom
CitationJournal: PLoS Biol / Year: 2020
Title: Dynamics in the murine norovirus capsid revealed by high-resolution cryo-EM.
Authors: Joseph S Snowden / Daniel L Hurdiss / Oluwapelumi O Adeyemi / Neil A Ranson / Morgan R Herod / Nicola J Stonehouse /
Abstract: Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically ...Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically challenging yet could be key for developing rational therapeutic agents to combat infections. Noroviruses are nonenveloped, icosahedral viruses of global importance to human health. They are a common cause of acute gastroenteritis, yet no vaccines or specific antiviral agents are available. Here, we use genetics and cryo-electron microscopy (cryo-EM) to study the high-resolution solution structures of murine norovirus as a model for human viruses. By comparing our 3 structures (at 2.9- to 3.1-Å resolution), we show that whilst there is little change to the shell domain of the capsid, the radiating protruding domains are flexible, adopting distinct states both independently and synchronously. In doing so, the capsids sample a range of conformational space, with implications for maintaining virion stability and infectivity.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)176,1023
Polymers176,1023
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10970 Å2
ΔGint-46 kcal/mol
Surface area58040 Å2
MethodPISA

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Components

#1: Protein Capsid protein / ORF2


Mass: 58700.598 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Murine norovirus 1 / References: 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: Murine norovirus 1 / Type: VIRUS / Details: RAW264.7 cells / Entity ID: all / Source: NATURAL
Source (natural)Organism: Murine norovirus 1 / Strain: CW1P3
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Mus musculus
Virus shellTriangulation number (T number): 3
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
1200 mMSodium chlorideNaCl1
25 mMMagnesium chlorideMgCl21
31 mMPotassium chlorideKCl1
41 mMCalcium chlorideCaCl21
510 mMHEPESC8H18N2O4S1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 281 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 FIELD
Image recordingElectron dose: 59.1 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7811 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 6C6Q

6c6q


Pdb chain-ID: A / Accession code: 6C6Q / Source name: PDB / Type: experimental model

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