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- PDB-8e2y: Purification of Enterovirus A71, strain 4643, WT capsid -

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Basic information

Entry
Database: PDB / ID: 8e2y
TitlePurification of Enterovirus A71, strain 4643, WT capsid
Components
  • Genome polyprotein
  • VP1
  • VP2
KeywordsVIRUS / enterovirus / thermostability / capsid
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsCatching, A. / Capponi, S. / Andino, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36178 United States
CitationJournal: Nat Commun / Year: 2023
Title: A tradeoff between enterovirus A71 particle stability and cell entry.
Authors: Adam Catching / Ming Te Yeh / Simone Bianco / Sara Capponi / Raul Andino /
Abstract: A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are ...A central role of viral capsids is to protect the viral genome from the harsh extracellular environment while facilitating initiation of infection when the virus encounters a target cell. Viruses are thought to have evolved an optimal equilibrium between particle stability and efficiency of cell entry. In this study, we genetically perturb this equilibrium in a non-enveloped virus, enterovirus A71 to determine its structural basis. We isolate a single-point mutation variant with increased particle thermotolerance and decreased efficiency of cell entry. Using cryo-electron microscopy and molecular dynamics simulations, we determine that the thermostable native particles have acquired an expanded conformation that results in a significant increase in protein dynamics. Examining the intermediate states of the thermostable variant reveals a potential pathway for uncoating. We propose a sequential release of the lipid pocket factor, followed by internal VP4 and ultimately the viral RNA.
History
DepositionAug 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Refinement description / Category: citation / citation_author / em_3d_fitting_list
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 / _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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)76,9813
Polymers76,9813
Non-polymers00
Water00
1
A: VP1
B: VP2
C: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)4,618,880180
Polymers4,618,880180
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: VP1
B: VP2
C: Genome polyprotein
x 5


  • icosahedral pentamer
  • 385 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)384,90715
Polymers384,90715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 462 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)461,88818
Polymers461,88818
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 VP1


Mass: 25366.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Cell line: RD cells / Cell line (production host): RD / Organ (production host): Muscle / Production host: Homo sapiens (human) / Strain (production host): RD / References: UniProt: F8SSP9
#2: Protein VP2


Mass: 25803.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD / Organ (production host): Muscle / Production host: Homo sapiens (human) / Strain (production host): RD / References: UniProt: W8XVV5
#3: Protein Genome polyprotein


Mass: 25811.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Cell line (production host): RD / Organ (production host): Muscle / Production host: Homo sapiens (human) / Strain (production host): RD / References: UniProt: W8XW58

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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: Human enterovirus 71 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Human enterovirus 71
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 6 sec. / Electron dose: 64.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
Image scansWidth: 6000 / Height: 4000

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
11RELION3.1final Euler assignment
12RELION3.1classification
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 20699
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1316 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation Coefficient
Atomic model buildingPDB-ID: 3VBS

3vbs


Accession code: 3VBS / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 146.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035420
ELECTRON MICROSCOPYf_angle_d0.6357412
ELECTRON MICROSCOPYf_dihedral_angle_d3.897725
ELECTRON MICROSCOPYf_chiral_restr0.044823
ELECTRON MICROSCOPYf_plane_restr0.008956

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