5AF2 | pdb_00005af2

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 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 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: https://doi.org/10.1002/prot.24794
  • Primary Citation Related Structures: 
    5AF2

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 68.61 kDa 
  • Atom Count: 5,361 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 572 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP3
A, B, C, D
143Rotavirus AMutation(s): 0 
EC: 2.7.7.50 (UniProt), 2.1.1.56 (UniProt), 3.1.4 (UniProt)
UniProt
Find proteins for A2T3S5 (Rotavirus A (isolate RVA/Monkey/South Africa/SA11-H96/1958/G3P5B[2]))
Explore A2T3S5 
Go to UniProtKB:  A2T3S5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2T3S5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free:  0.193 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.29α = 90
b = 74.96β = 112.8
c = 63.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2015-04-08
    Changes: Atomic model
  • Version 1.3: 2015-04-29
    Changes: Database references
  • Version 1.4: 2024-05-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Other