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- PDB-3j22: The Enterovirus 71 A-particle -

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Basic information

Entry
Database: PDB / ID: 3j22
TitleThe Enterovirus 71 A-particle
Components
  • capsid protein VP0
  • capsid protein VP1
  • capsid protein VP3
KeywordsVIRUS / EV71 / 135S
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHuman enterovirus 71
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsShingler, K.L.
CitationJournal: PLoS Pathog / Year: 2013
Title: The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating.
Authors: Kristin L Shingler / Jennifer L Yoder / Michael S Carnegie / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein /
Abstract: Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has ...Since its discovery in 1969, enterovirus 71 (EV71) has emerged as a serious worldwide health threat. This human pathogen of the picornavirus family causes hand, foot, and mouth disease, and also has the capacity to invade the central nervous system to cause severe disease and death. Upon binding to a host receptor on the cell surface, the virus begins a two-step uncoating process, first forming an expanded, altered "A-particle", which is primed for genome release. In a second step after endocytosis, an unknown trigger leads to RNA expulsion, generating an intact, empty capsid. Cryo-electron microscopy reconstructions of these two capsid states provide insight into the mechanics of genome release. The EV71 A-particle capsid interacts with the genome near the icosahedral two-fold axis of symmetry, which opens to the external environment via a channel ∼10 Å in diameter that is lined with patches of negatively charged residues. After the EV71 genome has been released, the two-fold channel shrinks, though the overall capsid dimensions are conserved. These structural characteristics identify the two-fold channel as the site where a gateway forms and regulates the process of genome release.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Other
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_database_related / pdbx_initial_refinement_model / pdbx_struct_oper_list
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 / _pdbx_database_related.content_type / _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
  • EMDB-5465
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  • Superimposition on EM map
  • EMDB-5465
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: capsid protein VP1
B: capsid protein VP0
C: capsid protein VP3


Theoretical massNumber of molelcules
Total (without water)77,4613
Polymers77,4613
Non-polymers00
Water0
1
A: capsid protein VP1
B: capsid protein VP0
C: capsid protein VP3
x 60


Theoretical massNumber of molelcules
Total (without water)4,647,659180
Polymers4,647,659180
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: capsid protein VP1
B: capsid protein VP0
C: capsid protein VP3
x 5


  • icosahedral pentamer
  • 387 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)387,30515
Polymers387,30515
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein VP1
B: capsid protein VP0
C: capsid protein VP3
x 6


  • icosahedral 23 hexamer
  • 465 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)464,76618
Polymers464,76618
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 capsid protein VP1 /


Mass: 25347.824 Da / Num. of mol.: 1 / Fragment: UNP residues 638-862 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
#2: Protein capsid protein VP0 / / capsid protein VP2


Mass: 25987.320 Da / Num. of mol.: 1 / Fragment: UNP residues 82-318 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
#3: Protein capsid protein VP3 /


Mass: 26125.834 Da / Num. of mol.: 1 / Fragment: UNP residues 324-562 / Source method: isolated from a natural source / Source: (natural) Human enterovirus 71 / References: UniProt: B2ZUN0
Sequence detailsTHE MODELED PROTEIN SEQUENCE WAS DERIVED FROM PDB ENTRY 3VBU.

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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 A-Particle / Type: VIRUS
Details: Icosahedral virus. The sample was purified mature virus heated in solution.
Molecular weightValue: 7 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.5 / Details: 10 mM Tris-HCL, 20 mM NaCl, 5 mM MgCl2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10 mM Tris-HCL, 20 mM NaCl, 5 mM MgCl2
Specimen supportDetails: glow discharged holey carbon Quantifoil electron microscopy grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temp: 76 K / Humidity: 95 % / Details: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Apr 17, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 4280 nm / Nominal defocus min: 1730 nm / Cs: 2 mm / Astigmatism: CTFFIND3 (EMAN) / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 40
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3Auto3DEM3D reconstruction
4EMAN23D reconstruction
CTF correctionDetails: auto3DEM
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Common Lines / Resolution: 6.3 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 11436 / Nominal pixel size: 1.27 Å / Actual pixel size: 1.27 Å
Details: A single data set was used for the reconstruction. Particles were selected using an automatic selection program (EMAN).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient
Details: METHOD--local refinement REFINEMENT PROTOCOL--rigid body DETAILS--One protomer was fit in Chimera, used to generate a full crystal map, then docked as a rigid body using Situs into the cryoEM density map
Atomic model buildingPDB-ID: 3VBU
Accession code: 3VBU / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5397 0 0 0 5397

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