5AF2

Crystal structure of the C-terminal 2',5'-phosphodiesterase domain of group A rotavirus protein VP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the C-Terminal 2',5'-Phosphodiesterase Domain of Group a Rotavirus Protein Vp3.

Brandmann, T.Jinek, M.

(2015) Proteins 83: 997

  • DOI: 10.1002/prot.24794

  • PubMed Abstract: 
  • In response to viral infections, the mammalian innate immune system induces the production of the second messenger 2'-5' oligoadenylate (2-5A) to activate latent ribonuclease L (RNase L) that restricts viral replication and promotes apoptosis. A subs ...

    In response to viral infections, the mammalian innate immune system induces the production of the second messenger 2'-5' oligoadenylate (2-5A) to activate latent ribonuclease L (RNase L) that restricts viral replication and promotes apoptosis. A subset of rotaviruses and coronaviruses encode 2',5'-phosphodiesterase enzymes that hydrolyze 2-5A, thereby inhibiting RNase L activation. We report the crystal structure of the 2',5'-phosphodiesterase domain of group A rotavirus protein VP3 at 1.39 Å resolution. The structure exhibits a 2H phosphoesterase fold and reveals conserved active site residues, providing insights into the mechanism of 2-5A degradation in viral evasion of host innate immunity.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP3
A, B, C, D
143Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2])Mutation(s): 0 
Find proteins for A2T3S5 (Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2]))
Go to UniProtKB:  A2T3S5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
A
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.290α = 90.00
b = 74.960β = 112.80
c = 63.220γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Database references
  • Version 1.2: 2015-04-08
    Type: Atomic model
  • Version 1.3: 2015-04-29
    Type: Database references