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 6JHT | pdb_00006jht

The cryo-EM structure of HAV bound to a neutralizing antibody-F9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6JHT

This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors.

Cao, L., Liu, P., Yang, P., Gao, Q., Li, H., Sun, Y., Zhu, L., Lin, J., Su, D., Rao, Z., Wang, X.

(2019) PLoS Biol 17: e3000229-e3000229

  • DOI: https://doi.org/10.1371/journal.pbio.3000229
  • Primary Citation Related Structures: 
    6JHQ, 6JHR, 6JHS, 6JHT

  • PubMed Abstract: 

    Hepatitis A virus (HAV), an enigmatic and ancient pathogen, is a major causative agent of acute viral hepatitis worldwide. Although there are effective vaccines, antivirals against HAV infection are still required, especially during fulminant hepatitis outbreaks. A more in-depth understanding of the antigenic characteristics of HAV and the mechanisms of neutralization could aid in the development of rationally designed antiviral drugs targeting HAV. In this paper, 4 new antibodies-F4, F6, F7, and F9-are reported that potently neutralize HAV at 50% neutralizing concentration values (neut50) ranging from 0.1 nM to 0.85 nM. High-resolution cryo-electron microscopy (cryo-EM) structures of HAV bound to F4, F6, F7, and F9, together with results of our previous studies on R10 fragment of antigen binding (Fab)-HAV complex, shed light on the locations and nature of the epitopes recognized by the 5 neutralizing monoclonal antibodies (NAbs). All the epitopes locate within the same patch and are highly conserved. The key structure-activity correlates based on the antigenic sites have been established. Based on the structural data of the single conserved antigenic site and key structure-activity correlates, one promising drug candidate named golvatinib was identified by in silico docking studies. Cell-based antiviral assays confirmed that golvatinib is capable of blocking HAV infection effectively with a 50% inhibitory concentration (IC50) of approximately 1 μM. These results suggest that the single conserved antigenic site from complete HAV capsid is a good antiviral target and that golvatinib could function as a lead compound for anti-HAV drug development.


  • Organizational Affiliation: 
    • CAS Key Laboratory of Infection and Immunity, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 130.63 kDa 
  • Atom Count: 8,959 
  • Modeled Residue Count: 1,152 
  • Deposited Residue Count: 1,180 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP1278Human hepatitis A virus Hu/Australia/HM175/1976Mutation(s): 0 
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08617
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VP2222Human hepatitis A virus Hu/Australia/HM175/1976Mutation(s): 0 
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08617
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VP3246Human hepatitis A virus Hu/Australia/HM175/1976Mutation(s): 0 
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08617
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB Light Chain213Human hepatitis A virus Hu/Australia/HM175/1976Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
FAB Heavy Chain221Human hepatitis A virus Hu/Australia/HM175/1976Mutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31570717
National Science Foundation (China)China31800145
National Science Foundation (China)China31370735

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection