8W9G | pdb_00008w9g

Hepatitis B virus core protein Y132A mutant in complex with CBT-078

• PDB DOI: https://doi.org/10.2210/pdb8W9G/pdb

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


• Deposited: 2023-09-05 Released: 2024-09-11 
• Deposition Author(s): Iwasaki, W., Katsura, K., Tomabechi, Y., Niwa, H., Ogawa, K., Kojima, S., Shirouzu, M.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 

Starting Model: experimental

Literature

Screening systems for the detection of hepatitis B virus replication and capsid assembly

Ogawa, K., Furutani, Y., Iwasaki, W., Katsura, K., Tomabechi, Y., Kojima, S., Shirouzu, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 107.12 kDa 
• Atom Count: 7,440 
• Modeled Residue Count: 892 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D, E, F	155	Hepatitis B virus subtype adyw	Mutation(s): 1
UniProt
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
5PT	G [auth A], H [auth A], I [auth B], J [auth C], K [auth D], L [auth E]	2-fluoranyl-N1-(4-fluorophenyl)-N3-(2-methylphenyl)benzene-1,3-dicarboxamide C21 H16 F2 N2 O2 SMISTEYAZXJEGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.79	α = 68.26
b = 67.66	β = 69.71
c = 85.03	γ = 83.01

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Iwasaki, W., Katsura, K., Tomabechi, Y., Niwa, H., Ogawa, K., Kojima, S., Shirouzu, M.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21fk0310112

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary