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Yorodumi- EMDB-2434: Cryo-EM reconstruction of empty enterovirus 71 in complex with a ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2434 | |||||||||
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Title | Cryo-EM reconstruction of empty enterovirus 71 in complex with a neutralizing antibody E18 | |||||||||
Map data | Reconstruction of EV71 virions with bound E18 antibody. The antibody binding induced genome release from EV71 virions. | |||||||||
Sample |
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Keywords | EV71 / human / enterovirus 71 / virus / antibody / Fab / E18 / neutralizing / pathogen | |||||||||
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 | |||||||||
Biological species | Mus musculus (house mouse) / Human enterovirus 71 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Plevka P / Perera R / Cardosa J / Suksatu A / Kuhn RJ / Rossmann MG | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2014 Title: Neutralizing antibodies can initiate genome release from human enterovirus 71. Authors: Pavel Plevka / Pei-Yin Lim / Rushika Perera / Jane Cardosa / Ampa Suksatu / Richard J Kuhn / Michael G Rossmann / Abstract: Antibodies were prepared by immunizing mice with empty, immature particles of human enterovirus 71 (EV71), a picornavirus that causes severe neurological disease in young children. The capsid ...Antibodies were prepared by immunizing mice with empty, immature particles of human enterovirus 71 (EV71), a picornavirus that causes severe neurological disease in young children. The capsid structure of these empty particles is different from that of the mature virus and is similar to "A" particles encountered when picornaviruses recognize a potential host cell before genome release. The monoclonal antibody E18, generated by this immunization, induced a conformational change when incubated at temperatures between 4 °C and 37 °C with mature virus, transforming infectious virions into A particles. The resultant loss of genome that was observed by cryo-EM and a fluorescent SYBR Green dye assay inactivated the virus, establishing the mechanism by which the virus is inactivated and demonstrating that the E18 antibody has potential as an anti-EV71 therapy. The antibody-mediated virus neutralization by the induction of genome release has not been previously demonstrated. Furthermore, the present results indicate that antibodies with genome-release activity could also be produced for other picornaviruses by immunization with immature particles. | |||||||||
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_2434.map.gz | 23.9 MB | EMDB map data format | |
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Header (meta data) | emd-2434-v30.xml emd-2434.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | EMD-2434.png | 257 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2434 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2434 | HTTPS FTP |
-Related structure data
Related structure data | 4c0yMC 2397C 2436C 4c0uC 4c10C 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_2434.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of EV71 virions with bound E18 antibody. The antibody binding induced genome release from EV71 virions. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.48 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 : Reconstruction of empty human enterovirus 71 virions with bound F...
Entire | Name: Reconstruction of empty human enterovirus 71 virions with bound Fab fragment of antibody E18 |
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Components |
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-Supramolecule #1000: Reconstruction of empty human enterovirus 71 virions with bound F...
Supramolecule | Name: Reconstruction of empty human enterovirus 71 virions with bound Fab fragment of antibody E18 type: sample / ID: 1000 Oligomeric state: Icosahedral virus and 60 copies of bound Fab Number unique components: 2 |
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Molecular weight | Theoretical: 6.8 MDa |
-Supramolecule #1: Human enterovirus 71
Supramolecule | Name: Human enterovirus 71 / type: virus / ID: 1 / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes / Sci species serotype: EV-174 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 3.2 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 280 Å / T number (triangulation number): 1 |
-Macromolecule #1: Fab EV18/4/D6-1/F1/G9
Macromolecule | Name: Fab EV18/4/D6-1/F1/G9 / type: protein_or_peptide / ID: 1 / Name.synonym: E18 / Number of copies: 60 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: house mouse |
Molecular weight | Theoretical: 4.6 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 / Details: 10 mM Tris-HCl, pH 8.0, 0.5 M NaCl, and 1 mM EDTA |
Grid | Details: Quantifoin R1.2/1.3 Holey carbon 200Mesh |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 2 second before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 49500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Min: 95 K / Max: 120 K / Average: 119 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Date | Sep 10, 2013 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 112 / Average electron dose: 18 e/Å2 / Bits/pixel: 16 |
-Image processing
CTF correction | Details: CTF determined for all particles from one film, phase flip |
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Final two d classification | Number classes: 44 |
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: eman, eman2 / Number images used: 418 |
Details | Particles were boxed with e2boxer.py |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: EMFit |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Rcrit |
Output model | PDB-4c0y: |