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Yorodumi- PDB-7cn2: Subparticle refinement of human papillomavirus type 16 pesudoviru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cn2 | ||||||
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Title | Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / Virus / immune complex / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | ||||||
Biological species | Human papillomavirus type 16 Oryctolagus cuniculus (rabbit) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å | ||||||
Authors | He, M.Z. / Li, S.W. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7cn2.cif.gz | 700.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cn2.ent.gz | 603 KB | Display | PDB format |
PDBx/mmJSON format | 7cn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cn2_validation.pdf.gz | 877.2 KB | Display | wwPDB validaton report |
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Full document | 7cn2_full_validation.pdf.gz | 926.5 KB | Display | |
Data in XML | 7cn2_validation.xml.gz | 113.3 KB | Display | |
Data in CIF | 7cn2_validation.cif.gz | 165.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/7cn2 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/7cn2 | HTTPS FTP |
-Related structure data
Related structure data | 30414MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Antibody | Mass: 11509.790 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #2: Antibody | Mass: 13212.764 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) #3: Protein | Mass: 56340.953 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 16 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: P03101 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: human papillomavirus type 16 pesudovirus in complex with H16.001 Fab Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Human papillomavirus type 16 |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3259: / Classification: refinement | |||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||
3D reconstruction | Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274860 / Symmetry type: POINT |