|Entry||Database: EMDB / ID: 8325|
|Title||Beta-propiolactone treated coxsackievirus A16 empty procapsid|
|Map data||Beta-propiolactone treated coxsackievirus A16 empty procapsid|
|Function / homology||Peptidase C3, picornavirus core protein 2A / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain ...Peptidase C3, picornavirus core protein 2A / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / RNA dependent RNA polymerase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / RNA helicase / Poliovirus 3A protein-like / 3C cysteine protease (picornain 3C) / T=pseudo3 icosahedral viral capsid / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphatase / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / suppression by virus of host gene expression / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / virion attachment to host cell / structural molecule activity / transcription, DNA-templated / RNA binding / membrane / ATP binding / Genome polyprotein|
Function and homology information
|Method||single particle reconstruction / cryo EM / 6.5 Å resolution|
|Authors||Chen F / Yao C|
|Citation||Journal: 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.
|Validation Report||PDB-ID: 5tsk|
About validation report
|Date||Deposition: Aug 12, 2016 / Header (metadata) release: Oct 12, 2016 / Map release: Feb 1, 2017 / Last update: Jun 13, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_8325.map.gz (map file in CCP4 format, 256001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.1 Å|
CCP4 map header:
-Entire COXSACKIEVIRUS A16
|Entire||Name: COXSACKIEVIRUS A16 / Number of components: 1|
|Mass||Theoretical: 5 MDa|
-Component #1: virus, COXSACKIEVIRUS A16
|Virus||Name: COXSACKIEVIRUS A16 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: SPECIES|
|Mass||Theoretical: 5 MDa|
|Species||Species: COXSACKIEVIRUS A16|
|Source (natural)||Host Species: Homo sapiens (human)|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.0032 mg/ml / pH: 7.6|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 12 K / Humidity: 1 % / Details: blot for 2 seconds|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 57000 X (nominal) / Cs: 0.007 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 70.0 - 90.0 K)|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 1350|
Details: Images were recorded on a Falcon II direct electron detector in the 18-frame movie mode
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 1642|
|3D reconstruction||Software: jspr|
CTF correction: CTF fitting was automatically performed using fitctf2.py program in jspr
Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF
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