3CM3 | pdb_00003cm3

High Resolution Crystal Structure of the Vaccinia Virus Dual-Specificity Phosphatase VH1

• PDB DOI: https://doi.org/10.2210/pdb3CM3/pdb

• Classification: HYDROLASE
• Organism(s): Vaccinia virus (strain Western Reserve)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-03-20 Released: 2009-02-10 
• Deposition Author(s): Koksal, A.C., Cingolani, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.185 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Dimeric Quaternary Structure of the Prototypical Dual Specificity Phosphatase VH1.

Koksal, A.C., Nardozzi, J.D., Cingolani, G.

(2009) J Biological Chem 284: 10129-10137

• PubMed: 19211553 
• DOI: https://doi.org/10.1074/jbc.M808362200
• Primary Citation Related Structures: 
  3CM3


• PubMed Abstract: 
  

  The Vaccinia virus H1 gene product, VH1, is a dual specificity phosphatase that down-regulates the cellular antiviral response by dephosphorylating STAT1. The crystal structure of VH1, determined at 1.32 A resolution, reveals a novel dimeric quaternary structure, which exposes two active sites spaced approximately 39 A away from each other. VH1 forms a stable dimer via an extensive domain swap of the N-terminal helix (residues 1-20). In vitro, VH1 can dephosphorylate activated STAT1, in a reaction that is competed by the nuclear transport adapter importin alpha5. Interestingly, VH1 is inactive with respect to STAT1 bound to DNA, suggesting that the viral phosphatase acts predominantly on the cytoplasmic pool of activated STAT1. We propose that the dimeric quaternary structure of VH1 is essential for specific recognition of activated STAT1, which prevents its nuclear translocation, thus blocking interferon-gamma signal transduction and antiviral response.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York 13210, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 20.51 kDa 
• Atom Count: 1,679 
• Modeled Residue Count: 164 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein phosphatase	A	176	N/A	Mutation(s): 1  Gene Names: H1 ORF, OPG106 EC: 3.1.3.48 (PDB Primary Data), 3.1.3 (PDB Primary Data)
UniProt
Find proteins for P07239 (Vaccinia virus (strain Western Reserve)) Explore P07239  Go to UniProtKB:  P07239

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME	C [auth A], D [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.185 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.816	α = 90
b = 38.69	β = 90
c = 134.987	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Koksal, A.C., Cingolani, G.

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description