5WTE | pdb_00005wte

Cryo-EM structure for Hepatitis A virus full particle

• PDB DOI: https://doi.org/10.2210/pdb5WTE/pdb
• EM Map EMD-6686: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Hepatovirus A
• Expression System: Chlorocebus aethiops
• Mutation(s): No 


• Deposited: 2016-12-11 Released: 2017-01-25 
• Deposition Author(s): Wang, X., Zhu, L., Dang, M., Hu, Z., Gao, Q., Yuan, S., Sun, Y., Zhang, B., Ren, J., Walter, T.S., Wang, J., Fry, E.E., Stuart, D.I., Rao, Z.
• Funding Organization(s): National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site

Wang, X., Zhu, L., Dang, M., Hu, Z., Gao, Q., Yuan, S., Sun, Y., Zhang, B., Ren, J., Kotecha, A., Walter, T.S., Wang, J., Fry, E.E., Stuart, D.I., Rao, Z.

(2017) Proc Natl Acad Sci U S A 114: 770-775

• PubMed: 28074040 
• DOI: https://doi.org/10.1073/pnas.1616502114
• Primary Citation Related Structures: 
  5WTE, 5WTF, 5WTG, 5WTH


• PubMed Abstract: 
  

  Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.

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Organizational Affiliation: 
• National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; [e-mail] [e-mail] [e-mail] [e-mail].
Division of Structural Biology, University of Oxford, Oxford OX3 7BN, United Kingdom.
National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China.
National Institutes for Food and Drug Control, Beijing 100050, China.
Sinovac Biotech Co., Ltd., Beijing 100085, China.
Division of Structural Biology, University of Oxford, Oxford OX3 7BN, United Kingdom; [e-mail] [e-mail] [e-mail] [e-mail].
Diamond Light Sources, Didcot OX11 0DE, United Kingdom.
Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 83.55 kDa 
• Atom Count: 5,706 
• Modeled Residue Count: 723 
• Deposited Residue Count: 746 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VP1	A	278	Hepatovirus A	Mutation(s): 0
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175)) Explore P08617  Go to UniProtKB:  P08617

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VP2	B	222	Hepatovirus A	Mutation(s): 0
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175)) Explore P08617  Go to UniProtKB:  P08617

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VP3	C	246	Hepatovirus A	Mutation(s): 0
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175)) Explore P08617  Go to UniProtKB:  P08617

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.3
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-01-25 
Deposition Author(s): Wang, X., Zhu, L., Dang, M., Hu, Z., Gao, Q., Yuan, S., Sun, Y., Zhang, B., Ren, J., Walter, T.S., Wang, J., Fry, E.E., Stuart, D.I., Rao, Z.

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Funding Organization	Location	Grant Number
National Science Foundation	China	31570717

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Other, Structure summary
• Version 1.2: 2017-02-08
  Changes: Database references
• Version 1.3: 2019-11-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-03-27
  Changes: Data collection, Database references, Derived calculations