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Yorodumi- EMDB-30415: The cryo-EM structure of human papillomavirus type 16 pesudovirus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30415 | |||||||||
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Title | The cryo-EM structure of human papillomavirus type 16 pesudovirus in complex with Fab H16.001 | |||||||||
Map data | The cryo-EM structure of human papillomavirus type 58 pseudovirus complexed with H16.001 Fab | |||||||||
Sample |
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Biological species | Human papillomavirus type 16 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||
Authors | He MZ / Li SW | |||||||||
Citation | Journal: NPJ Vaccines / Year: 2020 Title: Structural characterization of a neutralizing mAb H16.001, a potent candidate for a common potency assay for various HPV16 VLPs. Authors: Weijin Huang / Maozhou He / Tingting Ning / Jianhui Nie / Feng Zhang / Qingbing Zheng / Rui Zhang / Ying Xu / Ying Gu / Shaowei Li / Youchun Wang / Abstract: With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different ...With more human papillomavirus (HPV) virus-like particle (VLP) vaccines to hit the market in future, a monoclonal antibody (mAb) with preferably comparable reactivity against vaccines from different expression systems and bioprocesses is urgently needed for the potency characterization. Among all mAbs against HPV16 collected, rabbit mAb H16.001 is potently neutralizing with the highest affinity, recognizes an immune-dominant epitope, and can comparably react with HPV16 vaccines from various sources. Cryo-electron microscopic (cryo-EM) structure demonstrated that 360 H16.001 Fabs could bind to HPV16 capsid in preferable binding manner without steric hindrance between neighboring Fabs, potentially supporting its identification for VLP structural integrity and utility in monitoring VLP structural probity. This structural analysis indicated that mAb H16.001 afforded unbiased potency characterization for various HPV16 vaccines and was potential for use in vaccine regulation practice. This study also showed a model process for selecting suitable mAbs for potency assays of other vaccines. | |||||||||
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_30415.map.gz | 1.6 GB | EMDB map data format | |
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Header (meta data) | emd-30415-v30.xml emd-30415.xml | 7 KB 7 KB | Display Display | EMDB header |
Images | emd_30415.png | 295.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30415 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30415.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The cryo-EM structure of human papillomavirus type 58 pseudovirus complexed with H16.001 Fab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.128 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 : Human papillomavirus type 16
Entire | Name: Human papillomavirus type 16 |
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Components |
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-Supramolecule #1: Human papillomavirus type 16
Supramolecule | Name: Human papillomavirus type 16 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host system | Organism: Homo sapiens (human) |
-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 II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 30.0 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 | Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9162 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |