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- EMDB-2608: Cryo-EM study of insect cell-expressed Enterovirus 71 and Coxsack... -

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Entry
Database: EMDB / ID: EMD-2608
TitleCryo-EM study of insect cell-expressed Enterovirus 71 and Coxsackievirus A16 virus-like particles provides a structural basis for vaccine development
Map dataReconstruction of Coxsackievirus A16 virus-like particles
Sample
  • Sample: Coxsackievirus A16 virus-like particles
  • Virus: Human coxsackievirus A16
Biological speciesHuman coxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsGong M / Zhu H / Zhou J / Yang C / Feng J / Huang X / Ji G / Xu H / Zhu P
CitationJournal: J Virol / Year: 2014
Title: Cryo-electron microscopy study of insect cell-expressed enterovirus 71 and coxsackievirus a16 virus-like particles provides a structural basis for vaccine development.
Authors: Minqing Gong / Hongtao Zhu / Jun Zhou / Chunting Yang / Jing Feng / Xiaojun Huang / Gang Ji / Honglin Xu / Ping Zhu /
Abstract: Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the two most common etiological agents responsible for the epidemics of hand, foot, and mouth disease (HFMD), a childhood illness with ...Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) are the two most common etiological agents responsible for the epidemics of hand, foot, and mouth disease (HFMD), a childhood illness with occasional severe neurological complications. A number of vaccine candidates against EV71 or CA16 have been reported; however, no vaccine is currently available for clinical use. Here, we generated a secreted version of EV71 and CA16 virus-like particles (VLPs) using a baculovirus-insect cell expression system and reconstructed the three-dimensional (3D) structures of both VLPs by cryo-electron microscopy (cryo-EM) single-particle analysis at 5.2-Å and 5.5-Å resolutions, respectively. The reconstruction results showed that the cryo-EM structures of EV71 and CA16 VLPs highly resemble the recently published crystal structures for EV71 natural empty particles and CA16 135S-like expanded particles, respectively. Our cryo-EM analysis also revealed that the majority of previously identified linear neutralizing epitopes are well preserved on the surface of EV71 and CA16 VLPs. In addition, both VLPs were able to induce efficiently neutralizing antibodies against various strains of EV71 and CA16 viruses in mouse immunization. These studies provide a structural basis for the development of insect cell-expressed VLP vaccines and for a potential bivalent VLP vaccine against both EV71- and CA16-associated HFMD.
IMPORTANCE: The recent outbreaks of hand, foot, and mouth disease (HFMD) in the Asia Pacific region spurred the search for effective vaccines against EV71 and CA16 viruses, the two most common ...IMPORTANCE: The recent outbreaks of hand, foot, and mouth disease (HFMD) in the Asia Pacific region spurred the search for effective vaccines against EV71 and CA16 viruses, the two most common etiological agents responsible for HFMD. In this paper, we show that secreted versions of EV71 and CA16 VLPs generated in the baculovirus-insect cell expression system highly resemble the crystal structures of their viral conterparts and that the majority of previously identified linear neutralizing epitopes are well preserved on the VLP surfaces. In addition, the generated VLPs can efficiently induce neutralizing antibodies against various strains of EV71 and CA16 viruses in mouse immunization. These studies provide a structural basis for the development of insect cell-expressed VLP vaccines and for a potential bivalent VLP vaccine against both EV71- and CA16-associated HFMD.
History
DepositionMar 12, 2014-
Header (metadata) releaseApr 16, 2014-
Map releaseApr 16, 2014-
UpdateMay 14, 2014-
Current statusMay 14, 2014Processing site: PDBe / 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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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_2608.map.gz / Format: CCP4 / Size: 204.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Coxsackievirus A16 virus-like particles
Voxel sizeX=Y=Z: 0.933 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-14.40153885 - 8.726364139999999
Average (Standard dev.)0.0 (±0.99999982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin505050
Dimensions380380380
Spacing380380380
CellA=B=C: 354.54 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9330.9330.933
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z354.540354.540354.540
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS505050
NC/NR/NS380380380
D min/max/mean-14.4028.726-0.000

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Supplemental data

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Sample components

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Entire : Coxsackievirus A16 virus-like particles

EntireName: Coxsackievirus A16 virus-like particles
Components
  • Sample: Coxsackievirus A16 virus-like particles
  • Virus: Human coxsackievirus A16

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Supramolecule #1000: Coxsackievirus A16 virus-like particles

SupramoleculeName: Coxsackievirus A16 virus-like particles / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightExperimental: 5.7 MDa / Theoretical: 5.7 MDa

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Supramolecule #1: Human coxsackievirus A16

SupramoleculeName: Human coxsackievirus A16 / type: virus / ID: 1 / NCBI-ID: 31704 / Sci species name: Human coxsackievirus A16 / Sci species strain: 09-7 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Spodoptera frugiperda Sf9 / Recombinant plasmid: pFastBac Dual
Molecular weightExperimental: 5.7 MDa / Theoretical: 5.7 MDa
Virus shellShell ID: 1 / Diameter: 300 Å / T number (triangulation number): 3

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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

Concentration1.7 mg/mL
BufferpH: 7.4 / Details: 0.013M PBS
GridDetails: glow-discharged Quantifoil R2/1 300 mesh Cu grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMar 7, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: OTHER / Number images used: 21403

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: Chimera
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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