4WZN

CRYSTAL STRUCTURE OF THE 2B PROTEIN SOLUBLE DOMAIN FROM HEPATITIS A VIRUS

• PDB DOI:  https://doi.org/10.2210/pdb4WZN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human hepatitis A virus Hu/Australia/HM175/1976
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-20 Released: 2015-01-28 
• Deposition Author(s): Garriga, D., Vives-Adrian, L., Buxaderas, M., Ferreira-da-Silva, F., Almeida, B., Macedo-Ribeiro, S., Pereira, P.J., Verdaguer, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

Structural Basis for Host Membrane Remodeling Induced by Protein 2B of Hepatitis A Virus.

Vives-Adrian, L., Garriga, D., Buxaderas, M., Fraga, J., Pereira, P.J., Macedo-Ribeiro, S., Verdaguer, N.

(2015) J Virol 89: 3648-3658

• PubMed: 25589659 
• DOI: https://doi.org/10.1128/JVI.02881-14
• Primary Citation of Related Structures:  
  4WZN


• PubMed Abstract: 
  

The complexity of viral RNA synthesis and the numerous participating factors require a mechanism to topologically coordinate and concentrate these multiple viral and cellular components, ensuring a concerted function. Similarly to all other positive-strand RNA viruses, picornaviruses induce rearrangements of host intracellular membranes to create structures that act as functional scaffolds for genome replication. The membrane-targeting proteins 2B and 2C, their precursor 2BC, and protein 3A appear to be primarily involved in membrane remodeling. Little is known about the structure of these proteins and the mechanisms by which they induce massive membrane remodeling. Here we report the crystal structure of the soluble region of hepatitis A virus (HAV) protein 2B, consisting of two domains: a C-terminal helical bundle preceded by an N-terminally curved five-stranded antiparallel β-sheet that displays striking structural similarity to the β-barrel domain of enteroviral 2A proteins. Moreover, the helicoidal arrangement of the protein molecules in the crystal provides a model for 2B-induced host membrane remodeling during HAV infection.

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Related Citations: 

• CLONING, PURIFICATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF THE 2AB PROTEIN FROM HEPATITIS A VIRUS.
  Garriga, D., Vives-Adrian, L., Buxaderas, M., Ferreira-Da-Silva, F., Almeida, B., Macedo-Ribeiro, S., Pereira, P.J., Verdaguer, N.
  (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 10: 1224

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Organizational Affiliation: 

Institut de Biologia Molecular de Barcelona, CSIC, Parc Científic de Barcelona, Barcelona, Spain [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.48 kDa 
• Atom Count: 2,300 
• Modelled Residue Count: 280 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A, B	217	Human hepatitis A virus Hu/Australia/HM175/1976	Mutation(s): 0  EC: 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175)) Explore P08617  Go to UniProtKB:  P08617

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.42	α = 90
b = 90.42	β = 90
c = 73.43	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): Garriga, D., Vives-Adrian, L., Buxaderas, M., Ferreira-da-Silva, F., Almeida, B., Macedo-Ribeiro, S., Pereira, P.J., Verdaguer, N.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2015-03-18
  Changes: Database references
• Version 1.2: 2019-06-12
  Changes: Data collection, Database references