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Yorodumi- EMDB-9144: Negative Stain EM map of uncleaved H7 New York in complex with H7... -
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-Basic information
Entry | Database: EMDB / ID: EMD-9144 | |||||||||
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Title | Negative Stain EM map of uncleaved H7 New York in complex with H7.5 Fab | |||||||||
Map data | Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Ward AB / Turner HL | |||||||||
Citation | Journal: PLoS Biol / Year: 2019 Title: Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains. Authors: Hannah L Turner / Jesper Pallesen / Shanshan Lang / Sandhya Bangaru / Sarah Urata / Sheng Li / Christopher A Cottrell / Charles A Bowman / James E Crowe / Ian A Wilson / Andrew B Ward / Abstract: Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating ...Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy (cryoEM) to decipher the mechanism of action of a potent HA head-directed monoclonal antibody (mAb) bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, prefusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the prefusion conformation. The "breathing" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously. | |||||||||
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_9144.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-9144-v30.xml emd-9144.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_9144.png | 63.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9144 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9144 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9144.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.05 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 : Negative stain EM map of uncleaved H7 New York in complex with H7...
Entire | Name: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab |
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Components |
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-Supramolecule #1: Negative stain EM map of uncleaved H7 New York in complex with H7...
Supramolecule | Name: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: 293F |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Uranyl Formate |
Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: OTHER / Software - Name: EMAN2 (ver. 1.4) |
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Final angle assignment | Type: OTHER |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 17851 |