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- EMDB-5466: Cryo-electron microscopy reconstruction of the Enterovirus 71 emp... -

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Basic information

Entry
Database: EMDB / ID: EMD-5466
TitleCryo-electron microscopy reconstruction of the Enterovirus 71 empty capsid
Map dataReconstruction of the EV71 empty capsid.
Sample
  • Sample: Enterovirus 71 empty capsid
  • Virus: Human enterovirus 71
KeywordsEnterovirus 71 / EV71 / empty capsid / 80S
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 / host cell nucleus / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsShingler KL / Yoder JL / Carnegie MS / Ashley RE / Makhov AM / Conway JF / Hafenstein S
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 10, 2012-
Header (metadata) releaseApr 3, 2013-
Map releaseApr 3, 2013-
UpdateApr 17, 2013-
Current statusApr 17, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j23
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j23
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5466_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5466.map.gz / Format: CCP4 / Size: 147.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the EV71 empty capsid.
Voxel sizeX=Y=Z: 1.27 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.25461292 - 6.03537798
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions341341341
Spacing341341341
CellA=B=C: 433.07 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z341341341
origin x/y/z0.0000.0000.000
length x/y/z433.070433.070433.070
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS341341341
D min/max/mean-3.2556.0350.000

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Supplemental data

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Sample components

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Entire : Enterovirus 71 empty capsid

EntireName: Enterovirus 71 empty capsid
Components
  • Sample: Enterovirus 71 empty capsid
  • Virus: Human enterovirus 71

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Supramolecule #1000: Enterovirus 71 empty capsid

SupramoleculeName: Enterovirus 71 empty capsid / type: sample / ID: 1000
Details: The sample was purified mature virus heated in solution.
Oligomeric state: icosahedral virus / Number unique components: 1
Molecular weightExperimental: 7 MDa / Theoretical: 7 MDa / Method: calculation

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Supramolecule #1: Human enterovirus 71

SupramoleculeName: Human enterovirus 71 / type: virus / ID: 1 / Name.synonym: EV71, Hand foot and mouth disease virus / Details: purified virus in solution / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Syn species name: EV71, Hand foot and mouth disease virus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 7 MDa / Theoretical: 7 MDa
Virus shellShell ID: 1 / Name: single capsid shell / Diameter: 300 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 10 mM Tris-HCl, 20 mM NaCl, 5 mM MgCl2
GridDetails: glow discharged holey carbon Quantifoil electron microscopy grids
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 4.37 µm / Nominal defocus min: 1.73 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 95 K
Alignment procedureLegacy - Astigmatism: CTFFIND3 (EMAN)
DateApr 17, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 40 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: auto3DEM
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2, auto3DEM / Details: A single data set was used for the reconstruction. / Number images used: 1931
DetailsThese particles were selected individually.

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Atomic model buiding 1

Initial modelPDB ID:

3vbu


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera, Situs
DetailsProtocol: rigid body. The protomer was fit in Chimera, used to generate a full crystal map, then docked as a rigid body in Situs.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j23:
The Enterovirus 71 empty capsid

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