6BVN

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


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid proteinA [auth C],
B,
C [auth A]
150Hepatitis B virus subtype adywMutation(s): 3 
UniProt
Find proteins for P03147 (Hepatitis B virus genotype D subtype adw (isolate United Kingdom/adyw/1979))
Explore P03147 
Go to UniProtKB:  P03147
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03147
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E9D
Query on E9D

Download Ideal Coordinates CCD File 
D [auth B]Heteroaryldihydropyrimidine tetramethylrodamine
C51 H48 Cl F N8 O7
PZTNESDVJNEZKJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI067417

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2022-04-13
    Changes: Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-05-15
    Changes: Data collection, Refinement description