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Yorodumi- EMDB-5671: Cross-Neutralizing Human Anti-Poliovirus Antibodies Bind the Reco... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5671 | |||||||||
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Title | Cross-Neutralizing Human Anti-Poliovirus Antibodies Bind the Recognition Site for Cellular Receptor | |||||||||
Map data | Cryo-EM reconstruction of type 2 polio virus with A12 Fab attached | |||||||||
Sample |
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Keywords | Polio / Type 2 Polio / A12 | |||||||||
Biological species | Human poliovirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.0 Å | |||||||||
Authors | Chen Z / Fischer ER / Kouiavskaia D / Hansen BT / Ludtke SJ / Bidzhieva B / Makiya M / Purcell RH / Chumakov K | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor. Authors: Zhaochun Chen / Elizabeth R Fischer / Diana Kouiavskaia / Bryan T Hansen / Steven J Ludtke / Bella Bidzhieva / Michelle Makiya / Liane Agulto / Robert H Purcell / Konstantin Chumakov / Abstract: Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of ...Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of human/chimpanzee anti-poliovirus antibodies and demonstrated that one of them, MAb A12, could neutralize polioviruses of both serotypes 1 and 2. This communication presents data on isolation of an additional cross-neutralizing antibody (F12) and identification of a previously unknown epitope on the surface of poliovirus virions. Epitope mapping was performed by sequencing of antibody-resistant mutants and by cryo-EM of complexes of virions with Fab fragments. The results have demonstrated that both cross-neutralizing antibodies bind the site located at the bottom of the canyon surrounding the fivefold axis of symmetry that was previously shown to interact with cellular poliovirus receptor CD155. However, the same antibody binds to serotypes 1 and 2 through different specific interactions. It was also shown to interact with type 3 poliovirus, albeit with about 10-fold lower affinity, insufficient for effective neutralization. Antibody interaction with the binding site of the cellular receptor may explain its broad reactivity and suggest that further screening or antibody engineering could lead to a universal antibody capable of neutralizing all three serotypes of poliovirus. | |||||||||
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_5671.map.gz | 11.6 MB | EMDB map data format | |
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Header (meta data) | emd-5671-v30.xml emd-5671.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_5671_1.jpg | 150.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5671 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5671 | HTTPS FTP |
-Validation report
Summary document | emd_5671_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_5671_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_5671_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5671 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5671 | HTTPS FTP |
-Related 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_5671.map.gz / Format: CCP4 / Size: 50.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of type 2 polio virus with A12 Fab attached | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.8 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 : Fab Fragment of A12 antibody bound to Type 2 poliovirus
Entire | Name: Fab Fragment of A12 antibody bound to Type 2 poliovirus |
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Components |
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-Supramolecule #1000: Fab Fragment of A12 antibody bound to Type 2 poliovirus
Supramolecule | Name: Fab Fragment of A12 antibody bound to Type 2 poliovirus type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: Human poliovirus 2
Supramolecule | Name: Human poliovirus 2 / type: virus / ID: 1 / NCBI-ID: 12083 / Sci species name: Human poliovirus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Grid | Details: 4 uL aliquots of sample were applied to freshly glow-discharged 200 mesh r2/2 Quantifoil copper grids suspended by forceps in the FEI Mark IV Vitrobot. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 65 K / Instrument: FEI VITROBOT MARK IV Method: Specimens were vitrified, after blotting for 2 seconds with a blot force of 5 at 80% relative humidity, by plunge freezing into liquid ethane. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 64 K / Max: 66 K / Average: 65 K |
Date | Mar 3, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 2 µm / Number real images: 150 / Average electron dose: 15 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 80173 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder: Liquid Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Particles with a defocus range of 1-5 um were boxed with EMAN2, and then processed using the standard single particle reconstruction procedure with full CTF correction. |
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CTF correction | Details: each image |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 1500 |
Final two d classification | Number classes: 10 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |