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Yorodumi- EMDB-0895: The cryo-EM structure of coxsackievirus A16 mature virion in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0895 | ||||||||||||||||||||||||||||||
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Title | The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab NA9D7 | ||||||||||||||||||||||||||||||
Map data | The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab NA9D7 | ||||||||||||||||||||||||||||||
Sample |
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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 / channel activity / protein complex oligomerization / 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 / channel activity / protein complex oligomerization / cytoplasmic vesicle membrane / monoatomic ion channel activity / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / monoatomic ion transmembrane transport / viral capsid / nucleoside-triphosphate phosphatase / symbiont-mediated suppression of host NF-kappaB cascade / host cell cytoplasm / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||||||||||||||
Biological species | Coxsackievirus A16 / Mus musculus (house mouse) | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||||||||||||||||||||||||||
Authors | He MZ / Xu LF / Zheng QB / Zhu R / Yin ZC / Cheng T / Li SW | ||||||||||||||||||||||||||||||
Funding support | China, United States, 9 items
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Citation | Journal: Cell Host Microbe / Year: 2020 Title: Identification of Antibodies with Non-overlapping Neutralization Sites that Target Coxsackievirus A16. Authors: Maozhou He / Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Zhenghui Zha / Yu Lin / Lisheng Yang / Yang Huang / Xiangzhong Ye / Shuxuan Li / Wangheng Hou / Yangtao Wu / Jinle Han / ...Authors: Maozhou He / Longfa Xu / Qingbing Zheng / Rui Zhu / Zhichao Yin / Zhenghui Zha / Yu Lin / Lisheng Yang / Yang Huang / Xiangzhong Ye / Shuxuan Li / Wangheng Hou / Yangtao Wu / Jinle Han / Dongxiao Liu / Zekai Li / Zhenqin Chen / Hai Yu / Yuqiong Que / Yingbin Wang / Xiaodong Yan / Jun Zhang / Ying Gu / Z Hong Zhou / Tong Cheng / Shaowei Li / Ningshao Xia / Abstract: Hand, foot, and mouth disease is a common childhood illness primarily caused by coxsackievirus A16 (CVA16), for which there are no current vaccines or treatments. We identify three CVA16-specific ...Hand, foot, and mouth disease is a common childhood illness primarily caused by coxsackievirus A16 (CVA16), for which there are no current vaccines or treatments. We identify three CVA16-specific neutralizing monoclonal antibodies (nAbs) with therapeutic potential: 18A7, 14B10, and NA9D7. We present atomic structures of these nAbs bound to all three viral particle forms-the mature virion, A-particle, and empty particle-and show that each Fab can simultaneously occupy the mature virion. Additionally, 14B10 or NA9D7 provide 100% protection against lethal CVA16 infection in a neonatal mouse model. 18A7 binds to a non-conserved epitope present in all three particles, whereas 14B10 and NA9D7 recognize broad protective epitopes but only bind the mature virion. NA9D7 targets an immunodominant site, which may overlap the receptor-binding site. These findings indicate that CVA16 vaccines should be based on mature virions and that these antibodies could be used to discriminate optimal virion-based immunogens. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0895.map.gz | 765.5 MB | EMDB map data format | |
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Header (meta data) | emd-0895-v30.xml emd-0895.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_0895.png | 273 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0895 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0895 | HTTPS FTP |
-Validation report
Summary document | emd_0895_validation.pdf.gz | 619.2 KB | Display | EMDB validaton report |
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Full document | emd_0895_full_validation.pdf.gz | 618.8 KB | Display | |
Data in XML | emd_0895_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_0895_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0895 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0895 | HTTPS FTP |
-Related structure data
Related structure data | 6lhqMC 0887C 0888C 0889C 0890C 0891C 0892C 0894C 0897C 0898C 6lhaC 6lhbC 6lhcC 6lhkC 6lhlC 6lhoC 6lhpC 6lhtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0895.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The cryo-EM structure of coxsackievirus A16 mature virion in complex with Fab NA9D7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Coxsackievirus A16 complex with Fab NA9D7
+Supramolecule #1: Coxsackievirus A16 complex with Fab NA9D7
+Supramolecule #2: Coxsackievirus A16
+Supramolecule #3: Fab NA9D7
+Macromolecule #1: VP1 protein
+Macromolecule #2: VP2 protein
+Macromolecule #3: VP3 protein
+Macromolecule #4: VP4 protein
+Macromolecule #5: light chain variable region of Fab NA9D7
+Macromolecule #6: heavy chain variable region of Fab NA9D7
+Macromolecule #7: SPHINGOSINE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45235 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |