Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 180-mer - A180 

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

Biological Assembly Evidence: microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 51.31 kDa 
• Atom Count: 3500 
• Residue Count: 432 
• Unique protein chains: 1

6BVN

Cryo-EM Structure of Hepatitis B virus T=3 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA

• DOI: 10.2210/pdb6BVN/pdb
• EMDataResource: EMD-7295

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Hepatitis B virus subtype adyw
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-12-13 Released: 2018-02-07 
• Deposition Author(s): Schlicksup, C., Wang, J.C., Zlotnick, A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids.

Schlicksup, C.J., Wang, J.C., Francis, S., Venkatakrishnan, B., Turner, W.W., VanNieuwenhze, M., Zlotnick, A.

(2018) Elife 7

• PubMed: 29377794 
• DOI: 10.7554/eLife.31473
• Primary Citation of Related Structures:  
  6BVF, 6BVN


• PubMed Abstract: 
  

Defining mechanisms of direct-acting antivirals facilitates drug development and our understanding of virus function. Heteroaryldihydropyrimidines (HAPs) inappropriately activate assembly of hepatitis B virus (HBV) core protein (Cp), suppressing formation of virions. We examined a fluorophore-labeled HAP, HAP-TAMRA. HAP-TAMRA induced Cp assembly and also bound pre-assembled capsids. Kinetic and spectroscopic studies imply that HAP-binding sites are usually not available but are bound cooperatively. Using cryo-EM, we observed that HAP-TAMRA asymmetrically deformed capsids, creating a heterogeneous array of sharp angles, flat regions, and outright breaks. To achieve high resolution reconstruction (<4 Å), we introduced a disulfide crosslink that rescued particle symmetry. We deduced that HAP-TAMRA caused quasi-sixfold vertices to become flatter and fivefold more angular. This transition led to asymmetric faceting. That a disordered crosslink could rescue symmetry implies that capsids have tensegrity properties. Capsid distortion and disruption is a new mechanism by which molecules like the HAPs can block HBV infection.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C	150	Hepatitis B virus subtype adyw	Mutation(s): 3  Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979)) Explore P03147  Go to UniProtKB:  P03147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E9D	B	Heteroaryldihydropyrimidine tetramethylrodamine C51 H49 Cl F N8 O7 XAATXQKIZWYMQM-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-13 
• Released Date: 2018-02-07 
Deposition Author(s): Schlicksup, C., Wang, J.C., Zlotnick, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI067417

Revision History 

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence