7CN2 | pdb_00007cn2

Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7CN2

This is version 1.3 of the entry. See complete history

Literature

Structural characterization of a neutralizing mAb H16.001, a potent candidate for a common potency assay for various HPV16 VLPs.

Huang, W.He, M.Ning, T.Nie, J.Zhang, F.Zheng, Q.Zhang, R.Xu, Y.Gu, Y.Li, S.Wang, Y.

(2020) NPJ Vaccines 5: 89-89

  • DOI: https://doi.org/10.1038/s41541-020-00236-w
  • Primary Citation Related Structures: 
    7CN2

  • PubMed 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 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.


  • Organizational Affiliation
    • Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), No.31 Huatuo Street, Daxing District, 102629 Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 486.38 kDa 
  • Atom Count: 32,841 
  • Modeled Residue Count: 4,233 
  • Deposited Residue Count: 4,410 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
The light chain variable region of H16.001 Fab fragment110Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
The heavy chain variable region of H16.001 Fab fragment120Oryctolagus cuniculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Major capsid protein L1505Human papillomavirus 16Mutation(s): 0 
Gene Names: L1
UniProt
Find proteins for P03101 (Human papillomavirus type 16)
Explore P03101 
Go to UniProtKB:  P03101
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03101
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.43 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcisTEM

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2021-03-17
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2025-06-18
    Changes: Data collection