6YGH | pdb_00006ygh

Duck hepatitis B virus capsid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6YGH

This is version 1.1 of the entry. See complete history

Literature

Slowly folding surface extension in the prototypic avian hepatitis B virus capsid governs stability.

Makbul, C.Nassal, M.Bottcher, B.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.57277
  • Primary Citation Related Structures: 
    6YGH, 6YGI

  • PubMed Abstract: 

    Hepatitis B virus (HBV) is an important but difficult to study human pathogen. Most basics of the hepadnaviral life-cycle were unraveled using duck HBV (DHBV) as a model although DHBV has a capsid protein (CP) comprising ~260 rather than ~180 amino acids. Here we present high-resolution structures of several DHBV capsid-like particles (CLPs) determined by electron cryo-microscopy. As for HBV, DHBV CLPs consist of a dimeric α-helical frame-work with protruding spikes at the dimer interface. A fundamental new feature is a ~ 45 amino acid proline-rich extension in each monomer replacing the tip of the spikes in HBV CP. In vitro, folding of the extension takes months, implying a catalyzed process in vivo. DHBc variants lacking a folding-proficient extension produced regular CLPs in bacteria but failed to form stable nucleocapsids in hepatoma cells. We propose that the extension domain acts as a conformational switch with differential response options during viral infection.


  • Organizational Affiliation
    • Julius Maximilian University of Würzburg, Department of Biochemistry and Rudolf Virchow Centre, Würzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 182.03 kDa 
  • Atom Count: 6,487 
  • Modeled Residue Count: 790 
  • Deposited Residue Count: 1,572 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein262Hepatitis B virus duck/DHBV-16Mutation(s): 0 
Gene Names: C
UniProt
Find proteins for P0C6J7 (Duck hepatitis B virus (strain United States/DHBV-16))
Explore P0C6J7 
Go to UniProtKB:  P0C6J7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6J7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBo1150/17-1
German Research Foundation (DFG)GermanyINST 93/903-1 FUGG
German Research Foundation (DFG)GermanyNa154/9-4

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection, Database references