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Yorodumi- EMDB-5673: Electron cryo-microscopy of enterovirus 71 complexed with a Fab f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5673 | |||||||||
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Title | Electron cryo-microscopy of enterovirus 71 complexed with a Fab fragment | |||||||||
Map data | Asymmetric reconstruction of ev71-Fab complex | |||||||||
Sample |
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Keywords | EV71 / enterovirus / HFMD / neutralizing antibody / Fab / cryoEM / strain-specific eptitope / VP1-145 | |||||||||
Biological species | Mus musculus (house mouse) / Human enterovirus 71 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 23.4 Å | |||||||||
Authors | Lee H / Cifuente JO / Ashley RE / Conway JF / Makhov AM / Tano Y / Shimizu H / Nishimura Y / Hafenstein S | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: A strain-specific epitope of enterovirus 71 identified by cryo-electron microscopy of the complex with fab from neutralizing antibody. Authors: Hyunwook Lee / Javier O Cifuente / Robert E Ashley / James F Conway / Alexander M Makhov / Yoshio Tano / Hiroyuki Shimizu / Yorihiro Nishimura / Susan Hafenstein / Abstract: Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 ...Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 induces severe neuropathology leading to high fatalities, especially among children under the age of 6 years. Currently, no established vaccines or treatments are available against EV71 infection. The monoclonal antibody MA28-7 neutralizes only specific strains of EV71 that have a conserved glycine at amino acid VP1-145, a surface-exposed residue that maps to the 5-fold vertex and that has been implicated in receptor binding. The cryo-electron microscopy structure of a complex between EV71 and the Fab fragment of MA28-7 shows that only one Fab fragment occupies each 5-fold vertex. A positively charged patch, which has also been implicated in receptor binding, lies within the Fab footprint. We identify the strain-specific epitope of EV71 and discuss the possible neutralization mechanisms of the antibody. | |||||||||
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_5673.map.gz | 78.7 MB | EMDB map data format | |
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Header (meta data) | emd-5673-v30.xml emd-5673.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_5673_1.jpg | 96.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5673 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5673 | HTTPS FTP |
-Validation report
Summary document | emd_5673_validation.pdf.gz | 317.8 KB | Display | EMDB validaton report |
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Full document | emd_5673_full_validation.pdf.gz | 317.4 KB | Display | |
Data in XML | emd_5673_validation.xml.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5673 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5673 | HTTPS FTP |
-Related structure data
Related structure data | 3j3zMC 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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-Map
File | Download / File: emd_5673.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Asymmetric reconstruction of ev71-Fab complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 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 : Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing...
Entire | Name: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody |
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Components |
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-Supramolecule #1000: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing...
Supramolecule | Name: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody type: sample / ID: 1000 / Number unique components: 2 |
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Molecular weight | Theoretical: 8.05 MDa |
-Supramolecule #1: Human enterovirus 71
Supramolecule | Name: Human enterovirus 71 / type: virus / ID: 1 / Name.synonym: EV71 / Details: Fab fragment is bound on the virus surface / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Sci species strain: 1095/Shiga / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: EV71 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 8 MDa |
Virus shell | Shell ID: 1 / Name: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1 |
-Macromolecule #1: MA28-7 neutralizing antibody Fab fragment
Macromolecule | Name: MA28-7 neutralizing antibody Fab fragment / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: BALB/c / synonym: mouse / Cell: hybridomas fused with myeloma cells |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2 |
Grid | Details: glow-discharged holey carbon Quantifoil electron microscopy grids |
Vitrification | Cryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 76 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 95 K |
Date | Feb 2, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 45 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 48425 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 6.12 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Selected particles were low-pass filtered at 10 Angstrom. Asymmetric reconstruction was performed with breaksym option in EMAN2. |
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CTF correction | Details: Each image |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations. Number images used: 27026 |
Final two d classification | Number classes: 2300 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L |
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Software | Name: Chimera |
Details | The Fab structure was fitted manually, then refined in Chimera. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
Output model | PDB-3j3z: |