Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 240-mer - A240 

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

Macromolecule Content

• Total Structure Weight: 68.14 kDa 
• Atom Count: 4544 
• Residue Count: 563 
• Unique protein chains: 1

4G93

CRYSTAL STRUCTURE OF THE HUMAN HEPATITIS B VIRUS T = 4 CAPSID, ADYW STRAIN, in COMPLEX WITH THE PHENYLPROPENAMIDE ASSEMBLY ACCELERATOR AT-130

• DOI: 10.2210/pdb4G93/pdb

• Classification: virus/inhibitor
• Organism(s): Hepatitis B virus subtype adyw
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-07-23 Released: 2013-07-24 
• Deposition Author(s): Katen, S.P., Zlotnick, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.383 
• R-Value Work: 0.379 
• R-Value Observed: 0.379 

Literature

Assembly-directed antivirals differentially bind quasiequivalent pockets to modify hepatitis B virus capsid tertiary and quaternary structure.

Katen, S.P., Tan, Z., Chirapu, S.R., Finn, M.G., Zlotnick, A.

(2013) Structure 21: 1406-1416

• PubMed: 23871485 
• DOI: 10.1016/j.str.2013.06.013
• Primary Citation of Related Structures:  
  4G93


• PubMed Abstract: 
  

Hepatitis B virus (HBV) is a major cause of liver disease. Assembly of the HBV capsid is a critical step in virus production and an attractive target for new antiviral therapies. We determined the structure of HBV capsid in complex with AT-130, a member of the phenylpropenamide family of assembly effectors. AT-130 causes tertiary and quaternary structural changes but does not disrupt capsid structure. AT-130 binds a hydrophobic pocket that also accommodates the previously characterized heteroaryldihydropyrimidine compounds but favors a unique quasiequivalent location on the capsid surface. Thus, this pocket is a promiscuous drug-binding site and a likely target for different assembly effectors with a broad range of mechanisms of activity. That AT-130 successfully decreases virus production by increasing capsid assembly rate without disrupting capsid structure delineates a paradigm in antiviral design, that disrupting reaction timing is a viable strategy for assembly effectors of HBV and other viruses.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D	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
0YP	B, C	N-[(1E)-1-bromo-1-(2-methoxyphenyl)-3-oxo-3-(piperidin-1-yl)prop-1-en-2-yl]-4-nitrobenzamide C22 H22 Br N3 O5 OQIUTYABZMBBME-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
0YP	Kd :  300000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 0.383 
• R-Value Work: 0.379 
• R-Value Observed: 0.379 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 527.379	α = 90
b = 362.754	β = 105.13
c = 538.226	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-23 
• Released Date: 2013-07-24 
Deposition Author(s): Katen, S.P., Zlotnick, A.

Revision History 

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Advisory, Refinement description