2ZTN | pdb_00002ztn

Hepatitis E virus ORF2 (Genotype 3)

• PDB DOI: https://doi.org/10.2210/pdb2ZTN/pdb

• Classification: VIRUS
• Organism(s): Paslahepevirus balayani
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-10-08 Released: 2009-08-25 
• Deposition Author(s): Yamashita, T., Unno, H., Mori, Y., Li, T.C., Takeda, N., Matsuura, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.56 Å
• R-Value Free: 
  0.309 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.305 (Depositor), 0.303 (DCC) 

Literature

Biological and immunological characteristics of hepatitis E virus-like particles based on the crystal structure

Yamashita, T., Mori, Y., Miyazaki, N., Cheng, R.H., Yoshimura, M., Unno, H., Shima, R., Moriishi, K., Tsukihara, T., Li, T.C., Takeda, N., Miyamura, T., Matsuura, Y.

(2009) Proc Natl Acad Sci U S A 106: 12986-12991

• PubMed: 19620712 
• DOI: https://doi.org/10.1073/pnas.0903699106
• Primary Citation Related Structures: 
  2ZTN


• PubMed Abstract: 
  

  Hepatitis E virus (HEV) is a causative agent of acute hepatitis. The crystal structure of HEV-like particles (HEV-LP) consisting of capsid protein was determined at 3.5-A resolution. The capsid protein exhibited a quite different folding at the protruding and middle domains from the members of the families of Caliciviridae and Tombusviridae, while the shell domain shared the common folding. Tyr-288 at the 5-fold axis plays key roles in the assembly of HEV-LP, and aromatic amino acid residues are well conserved among the structurally related viruses. Mutational analyses indicated that the protruding domain is involved in the binding to the cells susceptive to HEV infection and has some neutralization epitopes. These structural and biological findings are important for understanding the molecular mechanisms of assembly and entry of HEV and also provide clues in the development of preventive and prophylactic measures for hepatitis E.

---

Organizational Affiliation: 
• Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

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

Macromolecule Content 

• Total Structure Weight: 51.61 kDa 
• Atom Count: 3,590 
• Modeled Residue Count: 472 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A	478	Paslahepevirus balayani	Mutation(s): 0
UniProt
Find proteins for Q9YLQ9 (Hepatitis E virus genotype 3 (isolate Human/United States/US2)) Explore Q9YLQ9  Go to UniProtKB:  Q9YLQ9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.56 Å
• R-Value Free:  0.309 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.305 (Depositor), 0.303 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 336.864	α = 90
b = 349.423	β = 90
c = 359.595	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Yamashita, T., Unno, H., Mori, Y., Li, T.C., Takeda, N., Matsuura, Y.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations