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- EMDB-8324: Beta-propiolactone treated coxsackievirus A16 mature virion -

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Basic information

Entry
Database: EMDB / ID: EMD-8324
TitleBeta-propiolactone treated coxsackievirus A16 mature virion
Map dataBeta-propiolactone treated coxsackievirus A16 mature virion
Sample
  • Virus: coxsackievirus A16
Biological speciescoxsackievirus A16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsChen F / Cong Y / Ye X / Huang Z
CitationJournal: J Virol / Year: 2017
Title: Beta-Propiolactone Inactivation of Coxsackievirus A16 Induces Structural Alteration and Surface Modification of Viral Capsids.
Authors: Chen Fan / Xiaohua Ye / Zhiqiang Ku / Liangliang Kong / Qingwei Liu / Cong Xu / Yao Cong / Zhong Huang /
Abstract: Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. ...Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. Here we present cryo-electron microscopy (cryo-EM) structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids at resolutions of 3.9 Å and 6.5 Å, respectively. Notably, both particles were found to adopt an expanded conformation resembling the 135S-like uncoating intermediate, with characteristic features including an opened 2-fold channel, the externalization of the N terminus of VP1 capsid protein, and the absence of pocket factor. However, major neutralizing epitopes are very well preserved on these particles. Further biochemical analyses revealed that BPL treatment impairs the abilities of CVA16 particles to bind to the attachment receptor heparan sulfate and to a conformation-dependent monoclonal antibody in a BPL dose-dependent manner, indicating that BPL is able to modify surface-exposed amino acid residues. Taken together, our results demonstrate that BPL treatment may induce alteration of the overall structure and surface properties of a nonenveloped viral capsid, thus revealing a novel mode of action of BPL. Beta-propiolactone (BPL) is commonly used as an inactivating reagent to produce viral vaccines. It is recognized that BPL inactivates viral infectivity through modification of viral nucleic acids. However, its effect on viral proteins remains largely unknown. Here, we present high-resolution cryo-EM structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids, which reveals an expanded overall conformation and characteristic features that are typical for the 135S-like uncoating intermediate. We further show that the BPL concentration affects the binding of inactivated CVA16 particles to their receptor/antibody. Thus, BPL treatment can alter the overall structure and surface properties of viral capsids, which may lead to antigenic and immunogenic variations. Our findings provide important information for future development of BPL-inactivated vaccines.
History
DepositionAug 12, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseFeb 1, 2017-
UpdateMay 2, 2018-
Current statusMay 2, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • 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_8324.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBeta-propiolactone treated coxsackievirus A16 mature virion
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.6402898 - 1.3746983
Average (Standard dev.)0.0007489143 (±0.09085825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z440.000440.000440.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-1.6401.3750.001

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Supplemental data

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Sample components

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Entire : coxsackievirus A16

EntireName: coxsackievirus A16
Components
  • Virus: coxsackievirus A16

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Supramolecule #1: coxsackievirus A16

SupramoleculeName: coxsackievirus A16 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 31704 / Sci species name: coxsackievirus A16 / Sci species strain: SZ05 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 5 MDa
Virus shellShell ID: 1 / Name: Capsid

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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

Concentration0.0032 mg/mL
BufferpH: 7.6 / Component - Concentration: 0.15 M / Component - Formula: PBS / Component - Name: phosphate buffered saline
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Details: blot for 2 seconds.

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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: 0.007 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 57000
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 90.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 3-18 / Number grids imaged: 1 / Number real images: 1350 / Average exposure time: 1.1 sec. / Average electron dose: 25.0 e/Å2
Details: Images were recorded on a Falcon II direct electron detector in the 18-frame movie mode.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25610
CTF correctionSoftware - Name: jspr
Software - details: CTF fitting was automatically performed using fitctf2.py program in jspr
Details: CTF fitting was automatically performed using fitctf2.py program in jspr
Startup modelType of model: INSILICO MODEL
In silico model: The data we performed the reference-free 2D analysis and initial model building utilizing EMAN2.1
Details: The data we performed the reference-free 2D analysis and initial model building utilizing EMAN2.1
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr
Details: In the 3D reconstruction process, the gold standard procedure was followed using jspr package
Number images used: 25610

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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