6BVF

Cryo-EM Structure of Hepatitis B virus T=4 capsid in complex with the fluorescent allosteric modulator HAP-TAMRA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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: --

  • DOI: 10.7554/eLife.31473
  • Primary Citation of Related Structures:  

  • 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 form ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A, B, C, D
150Hepatitis B virus genotype D subtype adwMutation(s): 3 
Gene Names: C
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw)
Go to UniProtKB:  P03147
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E9D
Query on E9D

Download SDF File 
Download CCD File 
B, C
Heteroaryldihydropyrimidine tetramethylrodamine
HAP-TAMRA
C51 H49 Cl F N8 O7
XAATXQKIZWYMQM-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States46-473-00

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Author supporting evidence